Experimental and theoretical investigations on the folding modes of depsipeptide molecules

The coupling of N-acyl-α-amino-acids with α-hydroxyacid-methyl amides results in depsipeptide molecules containing two chiral centers and one ester function inserted between two amide functions. Their conformational features have been investigated by IR spectroscopy, proton magnetic resonance, X-ray diffraction, and theoretical P.C.I.L.O. calculations. It is shown that most of these molecules are folded by an intramolecular 4 → 1 hydrogen bonding. Two folded conformations, similar to the well known β turn in peptides, are described, the stability of which depends on the configurational sequence in the investigated molecule. LL and LD species are folded in two different ways whereas LG sequences containing an achiral hydroxy-acid residue accommodate both of them. The presence of a N-terminal achiral amino acid noticeably decreases the folding ratio. The above conclusions are then compared with the conformational features of homologous tripeptide molecules.     

Experimental and theoretical studies of the structure of tellurate-borate glasses network

The structural properties of the xTeO₂·(1-x)B₂O₃ glasses (x = 0.6; 0.7) were investigated by FT-IR spectroscopy. From the analysis of the FTIR spectra, it is reasonable to assume that by the increasing of boron ions content, the tetrahedral [BO₄] units are gradually replaced by the trigonal [BO₃] units. The increase in the number of non-bridging oxygen atoms would decrease the connectivity of the glass network and will yield the depolymerization of the borate chains. The molecular structure and vibrational frequencies of the proposed structural models have been studied by exploring the density functional theory (DFT) calculations. The FTIR spectra of the xTeO₂·(1-x)B₂O₃ vitreous systems were compared with the calculated spectrum. This procedure allowed us to assign most of the observed IR bands.     

Experimental and theoretical investigations of spectroscopic properties of azobenzene derivatives in solution

The UV-Vis spectra of series of polymethylmethacrylate (PMMA) copolymers with attached trans-azobenzene derivatives were measured in 1,1,2-trichloroethane. In order to gain some insight into the recorded spectra, the quantum chemical calculations were performed for the substituted azobenzenes using both configuration interaction with single excitations method (CIS) as well as density functional theory (DFT) with B3LYP and PBE0 functionals. The calculations were performed in solvent. In particular, we found that the PBE0 excitation energies are in very good agreement with the experimental data. Figure The plots of orbital contour surfaces for molecule II. The molecular orbitals were calculated at the PBE0/6-311++G(d,p) level of theory. The upper plot presents contour surface of HOMO and the lower presents contour surface of LUMO. Shown are the contour surfaces of orbital amplitude 0.04 (red) and -0.04 (blue)     

Experimental and theoretical investigations on the validity of the geometrical optics model for calculating the stability of optical traps.

We have developed a computer program based on the geometrical optics approach proposed by Roosen to calculate the forces on dielectric spheres in focused laser beams. We have explicitly taken into account the polarization of the laser light and thd divergence of the laser beam. The model can be used to evaluate the stability of optical traps in a variety of different optical configurations. Our calculations explain the experimental observation by Ashkin that a stable single-beam optical trap, without the help of the gravitation force, can be obtained with a strongly divergent laser beam. Our calculations also predict a different trap stability in the directions orthogonal and parallel to the polarization direction of the incident light. Different experimental methods were used to test the predictions of the model for the gravity trap. A new method for measuring the radiation force along the beam axis in both the stable and instable regions is presented. Measurements of the radiation force on polystyrene spheres with diameters of 7.5 and 32 microns in a TEM00-mode laser beam showed a good qualitative correlation with the predictions and a slight quantitative difference. The validity of the geometrical approximations involved in the model will be discussed for spheres of different sizes and refractive indices.     

Experimental and theoretical investigations of submerged fermentation and synthesis of pectinolytic enzymes by Aspergillus niger

The growth of the microorganism and the production of the pectinolytic enzyme complex in a stirred 30-l biofermentor using the Aspergillus niger Rehbrücke strain were studied. The time courses of fermentation parameters (formation of biomass, consumption of carbon and inorganic nitrogen source, formation of pectinolytic enzymes) were measured. The formation of biomass showed a distinct lag phase, followed by a log phase with exponential growth and finally a stationary period when cell lysis was beginning. The uptake of the carbon source and inorganic nitrogen source by the A. niger cells corresponded to the time course of growth. The formation of pectinolytic enzymes took place in two steps. The first one was growth-bounded and finished with the end of the log phase of biomass growth. The second step of pectinolytic enzyme formation took place after the end of the catabolite repression of the carbon source and was not growth-bounded. On the basis of the experimental data a mathematical model of the fermentation process was developed. Comparison of the kinetics of the measured fermentation curves and the solution curves of the model showed qualitatively good agreement.     

Experimental and theoretical investigations of stochastic oscillatory phenomena in a nonrelativistic electron beam with a virtual cathode

Results are presented from experimental investigations of oscillatory phenomena in an electron beam with a virtual cathode in a diode gap with a decelerating field. Experiments have revealed a stochastic broadband generation of the microwave oscillations of a virtual cathode in a decelerating field. Numerical simulations based on a simple one-dimensional model have shown that the onset of the stochastic generation and the broadening of the oscillation spectrum with increasing beam deceleration rate are governed by the processes of regrouping of the electrons in a beam with a virtual cathode.     

Experimental and theoretical investigations of circular dichroism of donor-acceptor 1,1'-binaphthyls: influence of substitution on the coupling amplitude and cotton effect of the charge-transfer band

The electronic circular dichroism (CD) spectra of donor-acceptor binaphthyls were investigated experimentally and theoretically. The enantiomerically pure forms of 1-(2-methoxy-1-naphthyl)- and 1-(2,3-dimethoxy-1-naphthyl)-2-methylisoquinolinium tetrafluoroborates (DA and D'A) were prepared, and their UV-vis and CD spectra were compared. The donor-acceptor interaction was apparent from the absorption at longer wavelengths, whereas its strength was not very different from each other. In addition, very similar structures were obtained for the two aromatic planes in DA and D'A when the geometry was optimized by the density functional theory. The additional methoxy group in the latter spices scarcely disturbed the UV-vis spectrum but significantly affected the CD spectrum. Thus, the observed CD spectra were considerably different from each other, especially in the (1) B(b) band couplet, where the amplitude was reduced to almost one-fourth in D'A. The theoretical investigations led to the following conclusions: (1) The potential curve associated with the central C-C dihedral angle of 1,1'-binaphthyl is fairly flat at the bottom for both DA and D'A and freely rotating at an ambient temperature. The potential curve of D'A is, however, significantly different from that of DA, in which the curve is much steeper and biased to the s-cis side. As the observed CD spectrum is an ensemble of conformers of various dihedral angles, such difference in potential certainly affects the overall spectrum; (2) The additional methoxy group introduced at the 3-position effectively altered the CD spectral pattern, which was theoretically supported by the calculation at the RI-CC2/TZVPP level; (3) Consequently, the classical coupled oscillator theory, in which the angle between the transition dipole moments of two aromatic planes is solely considered, is not applicable to the quantitative evaluation of the chiroptical properties of 1,1'-binaphthyls; rather, the quantum chemical approach is preferred, permitting a direct comparison with the experiment.     

Experimental and theoretical studies on the excess capacity of Photosystem II

It has been recently suggested that compensatory changes in Photosystem II (PS II) electron turnover rates can protect photosynthesis from photoinhibition [Behrenfeld et al. (1998) Photosynth Res 58: 259–268]. We have further explored this feature of PS II using a rate electrode for simultaneous measurements of the steady-state rate of oxygen evolution and the oxygen flash yield depending on the background irradiance in both control and photoinhibited algal cells of Chlorella Böhm. Theoretical simulations based on the two-electron gate model agree qualitatively with experimental data if we assume an increase of the electron turnover rate in the remaining functional PS II centers of the photoinhibited sample. Our results confirm the hypothesis that the compensatory effect enables cells to maintain the maximal rates of photosynthesis even in the presence of moderate photoinhibition (decrease of up to 50% in the number of functional centers) and that the effect originates from the inner capacity of electron transport through PS II. The origin of the compensatory effect is briefly discussed.     

Experimental and theoretical investigations of novel oxidovanadium(IV) juglone complex: DNA/HSA interaction and cytotoxic activity

Abstract

A new oxidovanadium(IV) complex VO(L)(Jug) (HL = 5-methoxy-1,3-bis (1-methyl-1H-benzo[d]imidazol-2-yl)benzene, Jug?=?juglone) was synthesized and characterized. Interactions of the V(IV) complex with calf thymus DNA (CT DNA) and human serum albumin were studied using different techniques such as UV–vis and fluorescence emission spectroscopy. The experimental results were confirmed by the molecular docking study. The oxidovanadium(IV) complex can efficiently cleave pUC19 DNA in the presence of Hydrogen peroxide. Also, the in vitro cytotoxicity properties of the oxidovanadium(IV) complex was evaluated against MCF-7, HPG-2 and HT-29 cancer cell lines and HEK293 non-malignant fibroblasts were evaluated and compared with free ligands, VOSO₄ and cisplatin as reference drugs.

Communicated by Ramaswamy H. Sarma     

Experimental investigations on the backbone folding of proline-containing model tripeptides

Some proline-containing tripeptides with the general formulas R⁰CO-L -Pro-X-NHR³ (X = Gly,Sar,L -Ala,D -Ala) and R⁰CO-X-L -Pro-NHR³ (X = Gly,L -Ala,D -Ala) have been investigated in solution by ir and ¹H-nmr spectroscopies. Their favored conformational states depend mainly on both the primary structure and the chiral sequence of the molecules. In inert solvents the βII-folding mode is the most favored conformation for the L -Pro-D -Ala and L -Pro-Gly tripeptides, while the βII′-turn is largely preferred by D -Ala-L -Pro derivatives. Under the same conditions only about one-third of the whole conformers of L -Pro-L -Ala molecules adopts the βI-folding mode. Semiopened C₇C₅ and C₅C₇ conformations are appreciably populated in the L -Pro-L -Ala sequence, on the one hand, and in the Gly-L -Pro and L -Ala-L -Pro derivatives, on the other hand. In L -Pro-Sar and X-L -Pro models, the cis–trans isomerism around the middle tertiary amide function is observed. Thus cis L -Pro-Sar and L -Ala-L -Pro conformers are folded by an intramolecular i + 3 → i hydrogen bond, whereas cis D -Ala-L -Pro and Gly-L -Pro molecules accommodate an open conformation. In dimethylsulfoxide the βII- and βII′-folding modes are not essentially destabilized, as contrasted with the βI conformation, which is less populated. In water solution all the above-mentioned conformations, with the possible exception of the βII′-folding mode for D -Ala-L -Pro molecules, seem to vanish. Solute conformations are also compared with the crystal structures of four proline-containing tripeptides.