Friedemann W. Schneider

An ab initio study on excited and ground state properties of the organic fluorescence probe PRODAN

Abstract Contbrmational energies of PRODAN (6-Propionyl-2-(dimethylamino)-naphthalene) have been calculated by Hartree-Fock ab initio methods as a function of the twisting and wagging motion of the amino and the rotational motion of the propionyl group. In agreement with experimental data, PRODAN is found planar in its optimum geometry. The CIS method is used to compute molecular orbital energies, excitation energies and dipole moments in dependence of the rotational isomerization of the dimethylamino group. The calculations allow the peculiar fluorescence properties of PRODAN to be explained by the TICT model.

Memory effects and oscillations in single-molecule kinetics

An exactly solvable model for single-molecule kinetics is suggested, based on the following assumptions: (i) A single molecule can exist in different chemical states and the random transitions from one chemical state to another can be described by a local master equation with time-dependent transition rates. (ii) Because of conformational and other intramolecular fluctuations the rate coefficients in the master equation are random functions of time; their stochastic properties are represented in terms of a set of control parameters. We assume that the fluctuating rate coefficients fulfill a separability condition, that is, they are made up of the multiplicative contributions of two factors: (a) a universal factor, which depends on the vector of control parameters and is the same for all chemical transformation processes and (b) process-dependent factors, which depend on the initial and final chemical states of the molecule but are independent of the control parameters. For systems with two chemical states the condition of separability is automatically fulfilled. We introduce an intrinsic time scale, which makes it possible to compute theoretically various experimental observables, such as the correlation functions of the fluorescent signal. We analyze the connections between the condition of separability and detailed balance, and discuss the possible cause of chemical oscillations in single molecule kinetics. We show that the intrinsic dynamics of the molecule, expressed by the fluctuations of the control parameters, may lead to damped oscillations of the correlation functions of the fluorescent signal. The influence of the random fluctuations on the control parameters may be described by a renormalized master equation with nonfluctuating apparent rate coefficients. The apparent rate coefficients do not have to obey a condition of detailed balance, even though the real rate coefficients do obey such a condition. It follows that the renormalized master equation may have damped oscillatory solutions.

Oxidation of ascorbic acid by air oxygen catalyzed by copper(II) ions in batch and continuous flow stirred tank reactors: bistability, oscillations and stochastic resonance

We report various nonlinear phenomena observed in the oxidation of ascorbic acid (H2Asc) by molecular oxygen in the presence of copper(II) ions in a continuous flow stirred tank reactor (CSTR) as well as in a batch reactor (closed system). Transient irregular oscillations were observed in a batch reactor by varying the initial concentrations of H2Asc and copper(II) ions. The behavior of the system in a CSTR was studied by varying the flow rate (kf) and the inflow concentrations of H2Asc and copper(II) ions. At low inflow concentrations of copper(II) ions the system exhibits bistability and small amplitude regular oscillations. In a two-dimensional parametric plot with coordinates kf and [Cu2+]0 the regions of bistability and oscillations form a cross-shaped diagram if the inflow concentration of H2Asc is kept constant. For increasing values of kf oscillations emerge ia a Hopf bifurcation and disappear due to a homoclinic orbit. Simultaneously applied small amplitude periodic and stochastic perturbations imposed onto the flow rate close to the bistable region revealed the phenomenon of stochastic resonance, which is confirmed by an analysis of probability distribution functions, power spectra, and singular value decomposition.

Spatial entrainment of patterns during the polymerization of acrylamide in the presence of the methylene blue–sulfide chemical oscillator

Abstract Turing-like patterns formed during the polymerization of acrylamide in the presence of sulfide, methylene blue and molecular oxygen are presented. We propose a chemical model of the polymerization of acrylamide in the presence of sulfide and oxygen. The model explains the formation of Turing patterns in this system. The experimental process of pattern formation becomes light sensitive if methylene blue is added. A space-periodic perturbation may thus be introduced into the system and spatial entrainment effects can be studied. The perturbation was realized by imposing an illumination pattern upon the reactive layer: after mixing the gel components and the MBO system in a Petri dish, a mask made of transparent film was placed between the light source and the dish. At different perturbation wavelengths we observed synchronization with the perturbation as well as irregular responses.

Photochemical and Photobiotogical Studies with Acridine and Phenanthridine Hydroperoxides in Cell‐free DNA

Abstract— The acridine and phenanthridine hydroperoxides 3 and 7 were synthesized as photochemical hydroxyl radical sources for oxidative DNA damage studies. The generation of hydroxyl radicals upon UVA irradiation (Λ. = 350 nm) was verified by trapping experiments with 5,5‐di‐methyl‐1‐pyrroline N‐oxide and benzene. The enzymatic assays of the damage in cell‐free DNA from bacteriophage PM2 caused by the acridine and phenanthridine hydroperoxides 3 and 7 under near‐UVA irradiation revealed a wide range of DNA modifications. Particularly, extensive single‐strand break formation and DNA base modifications sensitive to formamidopyrimidine DNA glycosylase (Fpg protein) were observed. In the photooxida‐tion of calf thymus DNA, up to 0.69±0.03% 8‐oxo‐7,8‐dihydroguanine was formed by the hydroperoxides 3 and 7 on irradiation, whose yield was reduced up to 40% in the presence of the hydroxyl radical scavengers mannitol and fert‐butanol. The acridine and phenanthridine hydroperoxides 3 and 7 also induce DNA damage through the type I photooxidation process, for which photoinduced electron transfer from 2′‐deoxyguanosine to the singlet states of 3 and 7 was estimated by the Rehm‐Weller equation to possess a negative Gibbs free energy of cα ‐5 kcal/ mol. Control experiments with the sensitizers acridine 1 and the acridine alcohol 4 in calf thymus and PM2 DNA confirmed the photosensitizing propensity of the UVA‐ab‐sorbing chromophores. The present study emphasizes that for the development of selective and efficient photochemical hydroxyl radical sources, chromophores with low photosensitizing ability must be chosen to avoid type I and type II photooxidation processes.

Resonant chaos control by light in a chemiluminescent reaction

Abstract We present the resonant method of chaos control using light as the control parameter. The experiments have been carried out with the chemiluminescent Belousov–Zhabotinsky (BZ) reaction, which is catalyzed by a mixture of cerium and ruthenium (tris(2-2′-bipyridine)ruthenium(II) ([Ru(bpy 3 )] 2+ )) in a continuous-flow stirred tank reactor. The perturbation by light (470 nm) is applied in the form of rectangular light pulses at the absorption wavelength of [Ru(bpy 3 )] 2+ . Several unstable periodic orbits (UPO) of different periodicities (P1, P2 and P3) have been stabilized. It is demonstrated that the UPOs are embedded in the chaotic attractor. For simulations and tracking calculations, we use the 7-variable Montanator model by Gyorgyi and Field.

Photochemical and Photobiological Studies of a Furonaphthopyranone as a Benzo-spaced Psoralen Analog in Cell-free and Cellular DNA

Abstract— Photobiological activities of the benzo‐spaced psoralen analog furonaphthopyranone 3 have been investigated in cell‐free and cellular DNA. The molecular geometry parameters of 3 suggest that it should not form interstrand crosslinks with DNA. With cell‐free DNA no evidence for crosslinking but also not for monoadduct formation was obtained; rather, the unnatural furocoumarin 3 induces oxidative DNA modifications under near‐UVA irradiation. The enzymatic assay of the photosensitized damage in cell‐free PM2 DNA revealed the significant formation of lesions sensitive to formamidopyrimidine DNA glyco‐sylase (Fpg protein). In the photooxidation of calf thymus DNA by the furonaphthopyranone 3, 0.29±0.02% 8‐oxo‐7,8‐dihydroguanine (8‐oxoGua) was observed. With 2′‐deoxyguanosine (dGuo), the guanidine‐releasing photooxidation products oxazolone and oxoimidazolidine were formed predominately, while 8‐oxodGuo and 4‐HO‐8‐oxodGuo were obtained in minor amounts. The lack of a significant D2O effect in the photooxidation of DNA and dGuo reveals that singlet oxygen (type II process) plays a minor role; control experiments with tert‐butanol and mannitol confirm the absence of hydroxyl radicals as oxidizing species. The furonaphthopyranone 3 (Ered= ‐1.93±0.03V) should act in its singlet‐excited state as electron acceptor for the photooxidation of dGuo (δGETca– kcal/mol), which corroborates photoinduced electron transfer (type I) as a major DNA‐oxidizing mechanism. A comet assay in Chinese hamster ovary (CHO) AS52 cells demonstrated that the psoralen analog 3 damages cellular DNA upon near‐UVA irradiation; however, no photosensitized mutagenicity was observed in CHO AS52 cell cultures

Characteristic functional approach to multiplicative fractal noise with application to environmental fluctuations in nonlinear chemical systems far from equilibrium

We compute the characteristic functional of a nonlinear transformation of a set of random variables. The equation is applied to the study of fractal stochastic processes with multiplicative noise. For illustration we investigate two types of chemical systems subjected to environmental fluctuations. We analyze the interaction between the intrinsic chemical fluctuations and environmental noise and evaluate the stochastic properties of the system in the presence of multiplicative noise. For an autocatalytic reaction subjected to external noise and with Gaussian and generally non-Markovian multiplicative external noise the averaged joint probability density of concentrations displays long tails of the negative power law type, which are independent of the detailed properties of the noise. We also study the influence of multiplicative noise on a nonlinear chemical system with a stable limit cycle. In the presence of multiplicative noise the limit cycle collapses and the average trajectory in the composition space becomes a spiral. This effect is a temporal analog of Anderson localization. We evaluate the damping factors and localization times for different types of noise ranging from noise with infinite memory (static disorder) and noise with long memory (dynamic disorder with fractal noise) to Markovian noise (dynamic disorder with short memory).