Thermal cis–trans isomerization of cis–transoidal polyphenylacetylene

Solution and solid-state thermal cis-trans isomerization of cis–transoidal polyphenylacetylene was investigated. At temperatures higher than 120°C, cis-trans thermal isomerization in solution is accompanied by cyclization, aromatization, and scission of the polymer chain. Both spectral and kinetics data showed that at temperatures lower than 120°C, not only cis-trans thermal isomerization takes place but also intramolecular cyclization.     

Direct calculation of interconversion barriers in dynamic chromatography and electrophoresis: Isomerization of captopril

Dynamic capillary electrophoresis (DCE) and direct calculation of the rate constants of isomerization has been applied to determine the cis-trans isomerization barriers of the angiotensin-converting enzyme inhibitor captopril. The separation of the rotational cis-trans isomeric drug has been performed in an aqueous 50 mM borate buffer at pH 9.3. Interconversion profiles featuring plateau formation, peak-broadening, and peak coalescence were observed. To determine the rate constants of the forward and backward reaction (k(cis-->trans) and k(trans-->cis)) of the isomerization process in dynamic capillary electrophoresis, a novel straightforward calculation method using the experimental parameters plateau height, h(plateau), peak width at half height w(h), the total migration times of the cis-trans isomers t(R) and the electroosmotic break-through time t(0) as well as the peak ratio of the cis-trans isomers is presented for the first time. From temperature dependent measurements the rate constants k(cis-->trans) and k(trans-->cis) and the kinetic activation parameters DeltaG( not equal), DeltaH( not equal), and DeltaS( not equal) of the cis-trans isomerization of captopril were obtained. From the activation parameters the isomerization barriers of captopril at 37 degrees C under basic conditions were calculated to be DeltaG( not equal) (cis-->trans) = 90.3 kJ.mol(-1)and DeltaG( not equal) (trans-->cis) = 90.0 kJ.mol(-1*).     

A kinetic study on the conversion of cis-2-butene with deuterium on a Pd/Fe3O4 model catalyst

The conversion of cis-2-butene with deuterium over a well-defined Pd/Fe(3)O(4) model catalyst was studied by isothermal pulsed molecular beam (MB) experiments under ultra high vacuum conditions. This study focuses on the processes related to dissociative hydrogen adsorption and diffusion into the subsurface of Pd nanoparticles and their influence on the activity and selectivity toward competing cis-trans isomerization and hydrogenation pathways. The reactivity was studied both under steady state conditions and in the transient regime, in which the reaction takes place on a D-saturated catalyst, over a large range of reactant pressures and reaction temperatures. We show that large olefin coverages negatively affect the abundance of D species, as indicated by a reduction of both reaction rates under steady state conditions as compared to the transient reactivity on the catalyst pre-saturated with D(2). Limitations in D availability during the steady state lead to a very weak dependence of both reaction rates on the olefin pressure. In contrast, when the surface is initially saturated with D, the transient reaction rates of both pathways exhibit positive kinetic orders on the butene pressure. Cis-trans isomerization and hydrogenation show kinetic orders of +0.7 and +1.0 on the D(2) pressure, respectively. Increasing availability of D noticeably shifts the selectivity toward hydrogenation. These observations together with the analysis of the transient reaction behavior suggest that the activity and selectivity of the catalyst is strongly controlled by its ability to build up and maintain a sufficiently high concentration of D species under reaction conditions. The temperature dependence of the reaction rates indicates that higher activation energies are required for the hydrogenation pathway than for the cis-trans isomerization pathway, implying that different rate limiting steps are involved in the competing reactions.     

Isomerization of DNA-bound distilbazolium ligand induced by electron transfer from photoexcited tris(1,10-phenanthroline)Ru(II)

The ability of the DNA duplex to behave as an efficient organized medium for cis-trans isomerization induced by electron transfer (ET) has been explored. Isomerization studies, luminescence quenching and DNA photocleavage assays show that photoexcited Ru(1,10-phenanthroline [phen])3(2+) transfers an electron to E,Z1,4-bis[2-(1-methylpyridinium-4-yl)vinyl]benzene (E,Z pMPVB), which subsequently undergoes one-way isomerization to E,E pMPVB. The unusual feature of the system is manifested by the lack of friction that is usually imposed on the photoisomerizable ligand by highly organized media. The apparent rate of ET in DNA increases when compared with the homogeneous solution. However, after correction for the local concentration of the reagents onto the biopolymer, the rate constant becomes independent of the DNA concentration and is at least 4 x 10(2) times smaller than that in the homogeneous aqueous solution. Using the photoinduced isomerization system, a large enhancement in the efficiency of single-strand break formation was found in plasmid DNA over that for Ru(phen)3(+2) alone using irradiation at lambda > 480 nm.     

Conformational preferences and cis-trans isomerization of azaproline residue

The conformational study of N-acetyl-N'-methylamide of azaproline (Ac-azPro-NHMe, the azPro dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the effects of the replacement of the backbone CHalpha group by the nitrogen atom on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). The incorporation of the Nalpha atom into the prolyl ring results in the different puckering, backbone population, and barriers to prolyl cis-trans isomerization from those of Ac-Pro-NHMe (the Pro dipeptide). In particular, the azPro dipeptide has a dominant backbone conformation D (beta2) with the cis peptide bond preceding the azPro residue in both the gas phase and solution. This may be ascribed to the favorable electrostatic interaction or intramolecular hydrogen bond between the prolyl nitrogen and the amide hydrogen following the azPro residue and to the absence of the unfavorable interactions between electron lone pairs of the acetyl carbonyl oxygen and the prolyl Nalpha. This calculated higher population of the cis peptide bond is consistent with the results from X-ray and NMR experiments. As the solvent polarity increases, the conformations B and B* with the trans peptide bond become more populated and the cis population decreases more, which is opposite to the results for the Pro dipeptide. The conformation B lies between conformations D and A (alpha) and conformation B* is a mirror image of the conformation B on the phi-psi map. The barriers to prolyl cis-trans isomerization for the azPro dipeptide increase with the increase of solvent polarity, and the cis-trans isomerization proceeds through only the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond for the azPro dipeptide in the gas phase and in solution, as seen for the Pro dipeptide. The pertinent distance d(N...H-NNHMe) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure and the lower rotational barriers for the azPro dipeptide than those for the Pro dipeptide in the gas phase and in solution.     

光化学反应中的磁场效应 Ⅱ.电子转移光敏化1,2-二苯乙烯的顺反异构化反应

前文报道了外加磁场对吸附在硅胶表面上的芳砜光解反应的影响,本文报道外加磁场影响光化学反应的另一个例子——电子转移光敏化1,2-二苯乙烯的异构化。近年来电子转移光敏化反应引起了有机光化学家们的极大注意^[2]。一些异构化、重排、裂解、氧化反应都可以通过电子转移机理敏化。电子转移光敏化的机理可以用(1)描述。图中A和D分别代表电子的受体和给体。     

Ozone interaction with conjugated polymers—II. Polyphenylacetylene

Free-standing films of cis-transoidal polyphenylacetylene, when treated with ozonized air at 1–2% by weight O₃ concentration, undergo a cis-trans isomerization induced by ozone as shown by electronic spectra. Moreover, the presence of the radical cation of polyphenylacetylene can be observed during ozone addition. The cis-trans isomerization is also confirmed by FT-IR spectra of polyphenylacetylene ozonized in solution. Hydroperoxidic groups, as well as peroxidic and aldehydic, are observed by FT-IR spectroscopy on ozonized polyphenylacetylene; in addition, ozonide groups are clearly present. The kinetics of ozonization of cis-transoid and trans-cisoid polyphenylacetylene was followed by electronic spectroscopy. The curves obtained as a function of ozonization time have a characteristic sigmoid shape. Polyphenylacetylene reacts more slowly with ozone than with the isolated double bonds of cis-1,4-polyisoprene, and thus it cannot act as an antiozonant.     

Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions

Green fluorescent proteins (GFPs) are widely used as tools in biochemistry, cell biology, and molecular genetics due to their unusual optical spectroscopic characteristics. The spectrophotometric and fluorescence properties of GFPs are controlled by the protonation states and possibly cis-trans isomerization of the chromophore (p-hydroxybenzylideneimidazolinone). In this work, we have investigated electronic structures, liquid structures, and solvent shifts of the three possible protonated states (neutral, anionic, and zwitterionic) and their cis-trans isomerization of a model compound 4'-hydroxybenzylidene-2-methyl-imidazolin-5-one-3-acetate (HBMIA) in aqueous solutions. Our calculated results suggest that HBMIA could adopt both cis and trans conformations in a solution, and it exists in three different protonation states depending on the pH conditions. The absorption spectrum observed in neutral solution is thus assigned to the electronic excitations within the neutral form and the cis isomer of the zwitterionic form, while the absorption band at 425 nm in the basic solution is due to the excitations within the anionic form and the trans isomer of the zwitterionic form. Some technical problems related to the computation of electronic excitations within the HBMIA at the anionic state are also discussed.     

Volume-demanding cis-trans isomerization of 1,2-diaryl olefins in the solid state

Volume-demanding cis-trans photoisomerization of the aromatic substituted alkenes 1-3 in the solid state at room temperature and at 50 degrees C is presented. Alkene 3 did not undergo the cis-trans isomerization in the solid state either at room temperature or at 50 degrees C. The importance of the presence of void space near the reaction center to facilitate the large volume change during cis-trans photoisomerization is discussed.     

Conformational preferences of non-prolyl and prolyl residues

The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.     

Conformational preferences of pseudoproline residues

The conformational study on N-acetyl-N'-methylamides of oxazolidine and thiazolidine residues (Ac-Oxa-NHMe and Ac-Thz-NHMe) is carried out using ab initio HF and density functional B3LYP methods with the self-consistent reaction field method to explore the effects of the replacement of the C(gamma)H(2) group in the prolyl ring by oxygen or sulfur atoms on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). As the solvent polarity increases, the conformations C with the C7 intramolecular hydrogen bonds become depopulated, the PPII- or PPI-like conformations F become more populated, and the cis populations increase for both Oxa and Thz dipeptides, as found for the Pro dipeptide, although the populations of backbone conformations and puckerings are different in pseudoproline and proline dipeptides. As the increase of solvent polarity, the populations of the trans/up conformations decrease for Oxa and Thz dipeptides, but they increase for the Pro dipeptide. It is found that the cis-trans isomerization proceeds through the anticlockwise rotation with omega' approximately -60 degrees about the oxazolidyl peptide bond and the clockwise rotation with omega' approximately +120 degrees about the thiazolidyl peptide bond in the gas phase and in solution, whereas the clockwise rotation is preferred for the prolyl peptide bond. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of the prolyl nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure but the lower rotational barriers for Oxa and Thz dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized. The calculated cis populations and rotational barriers to the cis-trans isomerization for both Oxa and Thz dipeptides in chloroform and/or water are consistent with the experimental values.     

Regioselective cis-trans isomerization of arachidonic double bonds by thiyl radicals: the influence of phospholipid supramolecular organization

Trans unsaturated fatty acids in humans may be originated by two different contributions. The exogenous track is due to dietary supplementation of trans fats and the endogenous path deals with free-radical-catalyzed cis-trans isomerization of fatty acids. Arachidonic acid residue (5c,8c,11c,14c-20:4), which has only two out of the four double bonds deriving from the diet, was used to differentiate the two paths and to assess the importance of a radical reaction. A detailed study on the formation of trans phospholipids catalyzed by the HOCH2CH2S* radical was carried out on L-alpha-phosphatidylcholine from egg lecithin and 1-stearoyl-2-arachidonoyl-L-alpha-phosphatidylcholine (SAPC) in homogeneous solution or in large unilamellar vesicles (LUVET). Thiyl radicals were generated from the corresponding thiol by either gamma-irradiation or UV photolysis, and the reaction course was followed by GC, Ag/TLC, and 13C NMR analyses. The isomerization was found to be independent of cis double bond location (random process) in i-PrOH solution. In the case of vesicles, the supramolecular organization of lipids produced a dramatic change of the isomerization outcome: (i) in egg lecithin, the reactivity of arachidonate moieties is higher than that of oleate and linoleate residues, (ii) in the linoleate residues of egg lecithin, the 9t,12c-18:2 isomer prevailed on the 9c,12t-18:2 isomer (3:1 ratio), and (iii) a regioselective isomerization of SAPC arachidonate residues occurred in the 5 and 8 positions. This effect of "positional preference" indicates that thiyl radicals entering the hydrophobic region of the membrane bilayer start to isomerize polyunsaturated fatty acid residues having the double bonds nearest to the membrane surfaces. We propose that arachidonic acid and its trans isomers can function as biomarkers in membranes for distinguishing the two trans fatty acid-forming pathways.     

Low temperature high-performance liquid chromatography of cis-trans proline dipeptides

Isomeric dipeptides which contain proline at the C-terminus and undergo on-column cis-trans isomerization were separated by reversed-phase chromatography at subambient column temperature. Chromatography at low temperatures offers a convenient method for measuring the relative concentrations of the isomers and, thus, the calculation of the equilibrium constants for such cis-trans isomerization at various conditions of solvent, pH, and temperature. Pure fractions of the cis and trans isomers were collected and used in kinetic studies of the isomerization. High-performance liquid chromatography at temperatures near the freezing point of the eluent is a potentially useful tool for the study of a wide range of biochemical molecules.     

Conformational preferences of N-methoxycarbonyl proline dipeptide

The conformational study on N-methoxycarbonyl-L-proline-N'-methylamide (Moc-Pro-NHMe, prolylcarbamate) is carried out using ab initio HF and density functional B3LYP methods with the self-consistent reaction field method in the gas phase and in solution (chloroform, acetonitrile, and water). The replacement of the N-acetyl group by the N-methoxycarbonyl group results in the changes in conformational preferences, populations for backbone and prolyl puckering, and barriers to cis-trans isomerization of the prolyl residue in the gas phase and in solution, although there are small changes in the geometry of the prolyl peptide bond and the torsion angles of backbone and prolyl ring. The cis population increases with the increase of solvent polarity, as found for Ac-Pro-NHMe (prolylamide), but it is amplified by 9% in the gas phase and about 17% in solution for prolylcarbamate compared with those for prolylamide. It is found that the cis-trans isomerization for prolylcarbamate proceeds through the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond in the gas phase and in solution, as found for prolylamide. However, the rotational barriers to the cis-trans isomerization for prolylcarbamate are calculated to be 3.7-4.7 kcal/mol lower than those of prolylamide in the gas phase and in solution, and are found to be less sensitive to the solvent polarity. The calculated rotational barriers for prolylcarbamate in chloroform and water are in good agreement with the observed values. The shorter hydrogen-bond distance between the prolyl nitrogen and the amide H (H(NHMe)) of the NHMe group, the decrease in electron overlap of the prolyl C-N bond, and the favorable electrostatic interaction between the ester oxygen and the amide H(NHMe) for the transition state seem to play a role in lowering the rotational barrier of prolylcarbamate. The smaller molecular dipole moments of the ground- and transition-state structures for prolylcarbamate in the gas phase and in solution seem to be one of factors to make the rotational barrier less sensitive to the solvent polarity. As the solvent polarity increases (i.e., from the gas phase to chloroform to acetonitrile), the value of DeltaH(tc)(double dagger) decreases and the magnitude of DeltaS(tc)(double dagger) increases for prolylcarbamate, which results in a nearly constant value of the rotational barrier.     

Linoleic acid peroxidation vs. isomerization: a biomimetic model of free radical reactivity in the presence of thiols

Biomimetic models of free radical-induced transformation of polyunsaturated fatty acids, such as micelles and liposomes, have been used for the study of lipid peroxidation and lipid isomerization. Free radical reactivity of thiol compounds is the common link between the two processes, since lipid peroxidation is inhibited by thiols, due to their H-donation ability, whereas lipid isomerization is catalysed by S-centered radicals. In this paper the two processes are compared for the first time, in solution and under biomimetic conditions, demonstrating that hydroperoxides and trans lipids are formed to comparable extents as a result of oxidative free radical conditions. The biomimetic model of micelles of linoleic acid, prepared by addition of a non-ionic surfactant (TWEEN(?)-20) and 2-mercaptoethanol as the amphiphilic thiol, was irradiated by ionizing radiation up to 400 Gy under various conditions. In air-equilibrated solutions, the cis-trans isomerization process was observed with a catalytic cycle of 370 together with a substantial amount of hydroperoxides (LOOH). The effect of micelle size was also studied in order to envisage the effect of the supramolecular organization on the outcome of the two processes, and in particular, for the positional preference of the double bond isomerization.     

Conformational preferences and cis-trans isomerization of L-lactic acid residue

The conformational study on N-acetyl- N'-methylamide of l-lactic acid (Ac-Lac-NHMe, the Lac dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore its backbone conformational preferences and cis-trans isomerization for the depsipeptide with an ester bond in the gas phase and in solution. In the gas phase and in chloroform, the conformation tB with a trans depsipeptide bond is most preferred for the Lac dipeptide, whose backbone torsion angles are phi approximately -150 degrees and psi approximately -5 degrees , juxtaposed to those of the 3 10-helical structure. The larger shift in phi is brought to reduce the repulsion between the two carbonyl carbons of the acetyl and NHMe groups. However, the polyproline II-like tF conformation becomes more populated and the relative stability of conformation tB decreases significantly as the solvent polarity increases. This may be ascribed to weakening a C(5) hydrogen bond between the depsipeptidyl oxygen and the carboxyl amide hydrogen that plays a role in stabilizing the conformation tB in the gas phase and in chloroform. The cis populations about the depsipeptide bond are nearly negligible in the gas phase and in solution. The rotational barriers to the cis-trans isomerization of the depsipeptide bond for the Lac dipeptide are calculated to be about 11 kcal/mol, which is about half of those for the Ala dipeptide, although they increase somewhat with the increase of solvent polarity. The cis-trans isomerization of the depsipeptide bond proceeds through either clockwise or anticlockwise rotations with torsion angles of about +90 degrees or -90 degrees , respectively, in the gas phase and in solution, whereas it has been known that the isomerization proceeds through only the clockwise rotation for alanyl and prolyl peptide bonds. The pertinent distances between the depsipeptidyl oxygen and the carboxyl amide hydrogen can describe the role of this hydrogen bond in stabilizing the transition state structures in the gas phase and in solution.     

Noble reaction features of bromoborane in oxidative addition of B-Br σ-bond to [M(PMe3)2] (M=Pt or Pd): theoretical study

Through detailed calculations by density functional theory and second-order M?ller-Plesset perturbation theory (MP2) to fourth-order M?ller-Plesset perturbation theory including single, double, and quadruple excitations [MP4(SDQ)] methods, we investigated the oxidative addition of the B-Br bond of dibromo(trimethylsiloxy)borane [Br(2)B(OSiMe(3))] to Pt(0) and Pd(0) complexes [M(PMe(3))(2)] (M = Pt or Pd) directly yielding a trans bromoboryl complex trans-[MBr{BBr(OSiMe(3))}(PMe(3))(2)]. Two reaction pathways are found for this reaction: One is a nucleophilic attack pathway which directly leads to the trans product, and the other is a stepwise reaction pathway which occurs through successive cis oxidative addition of the B-Br bond to [M(PMe(3))(2)] and thermal cis-trans isomerization. In the Pt system, the former course occurs with a much smaller energy barrier (E(a) = 5.8 kcal/mol) than the latter one (E(a) = 20.7 kcal/mol), where the DFT-calculated E(a) value is presented hereafter. In the Pd system, only the latter course is found in which the rate-determining steps is the cis-trans isomerization with the E(a) of 15.1 kcal/mol. Interestingly, the thermal cis-trans isomerization occurs on the singlet potential energy surface against our expectation. This unexpected result is understood in terms of the strong donation ability of the boryl group. Detailed analyses of electronic processes in all these reaction steps as well as remarkable characteristic features of [Br(2)B(OSiMe(3))] are also provided.     

Investigation of tetherable distilbazolium compounds as fluorescent probes in nanostructured silica sol-gel materials

Distibazolium dyes are investigated by steady-state and time-resolved fluorescence techniques in a series of low- and high-viscosity polar solvents and in a silica sol-gel matrix. In all solvents and the sol-gel matrix, an interplay of photoinduced switching between different cis-trans isomers and solvation dynamics is observed. Even in a viscous solution (glycerol) and in silica gel, cis-trans isomerization is solvent-controlled. Whereas in glycerol the solvation results in a time-dependent fluorescence Stokes shift, the solvation-induced spectral heterogeneity in silica gel is mostly static, possibly due to a close proximity of dye molecules to the silica surfaces of the nanopores. Compared to low-viscosity solvents, where the cis-trans isomerization process takes place with a solvent-dependent rate on the timescale of about 120-150 ps, it slows down to about 1100-1400 ps in glycerol and about 1500 ps in a sol-gel matrix. Additionally, fluorescence kinetics of the dyes in the sol-gel reveals the presence of a range of different "frozen-in" conformers exhibiting a broad spectrum of lifetimes from 20 to 300 ps.     

Exploring the coordination chemistry of isomerizable terpyridine derivatives for successful analyses of cis and trans isomers by travelling wave ion mobility mass spectrometry

The photochemical cis-trans isomerization of the 4-{4-[2-(pyridin-4-yl)ethenyl]phenyl}-2,2':6',2'-terpyridine ligand (vpytpy) was investigated by UV-vis, NMR and TWIM-MS. Ion mobility mass spectrometry was performed pursuing the quantification of the isomeric composition during photolysis, however an in-source trans-to-cis isomerization process was observed. In order to overcome this inherent phenomenon, the isomerization of the vpytpy species was suppressed by complexation, reacting with iron(ii) ions, and forming the [Fe(vpytpy)(2)](2+) complex. The strategy of "freezing" the cis-trans isomerizable ligand at a given geometric conformation was effective, preventing further isomerization, thus allowing the distinction of each one of the isomers in the photolysed mixture. In addition, the experimental drift times were related to the calculated surface areas of the three possible cis-cis, cis-trans and trans-trans iron(ii) complex isomers. The stabilization of the ligand in a given conformation also allows us to obtain the cis-cis and cis-trans complexes exhibiting the ligand in the metastable cis-conformation, as well as in the thermodynamically stable trans-conformation.