Probing the photochemical mechanism in photoactive yellow protein

Selectively bridged model compounds related to the chromophore in photoactive yellow protein have been synthesized where the single bond adjacent to the benzene ring (bond 1) and where both bond 1 and the adjacent double bond (bond 2) are bridged. They were compared to the nonbridged reference compound regarding their photophysical properties using steady-state and time-resolved fluorescence at various temperatures. Quantum chemical calculations were additionally performed and showed that several conformers are populated in the ground state. The neutral model compounds show that the nonradiative deactivation channel is linked to both single- and double-bond twisting. The relative importance of single-bond twisting is increased for the corresponding deprotonated hydroxy compounds with an enhanced donor character. The simultaneous photochemical activity of both single and double bonds explains the ease of photochemical isomerization in the confined environment of the natural PYP protein and also of the primary step in the vision process in rhodopsin.     

Enantiomeric resolution of new aromatase inhibitors by liquid chromatography on cellulose chiral stationary phases

Analytical HPLC methods using derivatized cellulose chiral stationary phases were developed for the direct enantioseparation of substituted [1-(imidazo-1-yl)-1-phenylmethyl)]-benzothiazolinone and benzoxazolinone derivatives with one chiral center. Those analogues of fadrozole constitute new potent nonsteroidal inhibitors of aromatase (P450 arom). The separations were made using normal phase methodology with a mobile phase consisting of n-hexane-alcohol (ethanol, 1-propanol, or 2-propanol) in various proportions, and a silica-based cellulose tris-3,5-dimethylphenylcarbamate (Chiralcel OD-H), or tris-methylbenzoate (Chiralcel OJ). The effects of concentration of various aliphatic alcohols in the mobile phase were studied. A better separation was achieved on cellulose carbamate phase compared with the cellulose ester phase. The effects of structural features of the solutes along with the temperature of the column on the discrimination between the enantiomers were examined. Baseline separation (Rs > 1.5) was easily obtained in many cases.     

Discovering New Classes of <Emphasis Type="Italic">Brugia malayi</Emphasis> Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change

SLIDE software, which models the flexibility of protein and ligand side chains while docking, was used to screen several large databases to identify inhibitors of Brugia malayi asparaginyl-tRNA synthetase (AsnRS), a target for anti-parasitic drug design. Seven classes of compounds identified by SLIDE were confirmed as micromolar inhibitors of the enzyme. Analogs of one of these classes of inhibitors, the long side-chain variolins, cannot bind to the adenosyl pocket of the closed conformation of AsnRS due to steric clashes, though the short side-chain variolins identified by SLIDE␣apparently bind isosterically with adenosine. We hypothesized that an open conformation of the motif 2 loop also permits the long side-chain variolins to bind in the adenosine pocket and that their selectivity for Brugia relative to human AsnRS can be explained by differences in the sequence and conformation of this loop. Loop flexibility sampling using Rigidity Optimized Conformational Kinetics (ROCK) confirms this possibility, while scoring of the relative affinities of the different ligands by SLIDE correlates well with the compounds’ ranks in inhibition assays. Combining ROCK and SLIDE provides a promising approach for exploiting conformational flexibility in structure-based screening and design of species selective inhibitors.     

Specific features of UV-vis absorption spectra of cis- and trans-polythiophenes

UV-vis optical spectra of several polythiophene with number of dimers n=1, 5, 10, 15 for cis- and trans-forms were investigated. The study was done theoretically using semi-empirical AM1 (Austin Model 1) and PM3 (Parametric Method 3) methods with the appropriate molecular geometry optimization. The experimental UV-vis absorption spectra were used for verification of the both semi-empirical theoretical models. With the increasing number of dimers a red shift of the absorption edge was observed. Solvent does not play a crucial role on behavior of the absorption spectrum. A comparison of the both semi-empirical methods with the observed experimental absorption spectra is performed. Role of state dipole moments of the investigated polythiophenes in the behavior of the observed UV-vis spectra is discussed. Particular role of pi-conjugated bonds is demonstrated.     

Optical spectra of some 6-styrylo-1H-pyrazolo[3,4-b]quinolines

It was proposed a method of synthesis several 6-styrylo1-1H-pyrazolo[3,4-b]quinolines as promising material for optoelectronics. Particularly, 6-styryl-1,3-diphenyl-1H-pyrazolo[3,4-b]quinolines were prepared by Wadsworth-Emmons reaction. One of advantageous of these materials is stability of their optical spectra versus the possible cis- and trans-transformation. Theoretical and experimental studies of optical absorption and photoluminescence excitation spectra for styryloquinolines were done. They show that the AM1 semi-empirical method gives better results compared to other approaches. We have found that the solvents do not play a role in the behavior of the spectra. The backside-substituted groups do not influence substantially the observed optical spectra.     

Synthesis and Anti‐HIV‐1 Evaluation of New Sonogashira‐Modified Emivirine (MKC‐442) Analogues

The MKC‐442 analogue 6‐(3,5‐dimethylbenzyl)‐5‐ethyluracil substituted with a (propargyloxo)methyl group at N(1) has previously been found highly active against HIV‐1. The C?C bond in the substituent at N(1) is here utilized in a series of chemical reactions in order to develop new agents with higher activity against HIV‐1‐resistant mutants. The syntheses involved Pd‐catalyzed C,C‐coupling reactions, addition of disulfides, and click chemistry on the terminal C?C bond as well as addition of bromine to the so formed internal C?C bonds. Sonogashira coupling were performed with silyl‐derivatized iodobenzyl alcohols which, after deprotection, were oxidized to aldehydes by means of IBX. The isomeric alcohol 37 was obtained in the Sonogashira reaction of propargyl alcohol with the N(1)‐substituted (4‐iodobenzyloxy)methyl derivative of the above mentioned uracil. Compound 37 turned out to be the most effective compound against problematic HIV‐1 mutants. The general observation in the present work is that a combination of alkyne and aryl in the substituent at N(1) leads to highly active compounds against HIV‐1.     

Optical absorption of 1H-pyrazolo[3,4-b]quinoline and its derivatives

The results of experimental studies and quantum chemical simulations of the absorption spectra of 1H-pyrazolo[3,4-b]quinoline and its derivatives are presented. The quantum chemical calculations (semi-empirical AM1 and PM3 methods) show similarity in the absorption spectra of 1H-pyrazolo[3,4-b]quinoline and 1,3-dimethyl-1H-pyrazolo[3,4-b]quinoline which are characterized by five strong absorption bands in the spectral range 200-500 nm. A substitution of the methyl groups by at least one phenyl group causes the drastic changes of the absorption spectra mainly within the spectral range 240-370 nm. We attribute these differences to additional molecular double bonding segments C=C of the substituted phenyl groups, i.e. to pi --> pi* transitions. A comparison of measured and the calculated absorption spectra manifests quite satisfactory agreement for all compounds in the part regarding the spectral position of the first oscillator (absorption threshold). At the same time, the measured spectra demonstrate the considerable broadening practically of all absorption bands and even complete damping some of them in the case of phenyl derivatives. The experiments performed with highly and weakly polar organic solvents shows that the solvent effect on the absorption spectra is small. For this reason the discrepancies between the calculated and the measured spectra are attributed to electron-vibronic coupling as well as to rotational dynamics of phenyl rings.     

Photoluminescence of 1,3-Diphenyl-1H-pyrazolo[3,4-b]quinoline and its derivatives: Experiment and quantum chemical simulations

The optical absorption and photoluminescent spectra are studied in recently synthesized diphenyl pyrazoloquinolines (DPPQ): 1,3-diphenyl-1H-pyrazolo[3,4-b] quinoline and its 6-vinyl, 6-N,N-diphenyl, 6-methyl, 6-fluoro, 6-bromo and 6-chloro derivatives. The photoemission spectra are recorded in organic solvents of different polarity and found to be highly solvatochromic. The measured spectra are compared with the quantum chemical calculations performed by means of the semiempirical methods (AM1 or PM3) in combination with the equilibrium molecular conformation (EMC) in vacuo (T = 0 K, Γ = 0.12 eV) or MD simulations (T = 300 K). The broadening of absorption and emission bands and their red-shift with increasing of temperature may be well reproduced by MD simulations. The Stokes shift of the photoluminescent spectra is obtained by including vibrational modes into the emission equation. The quantum chemical method AM1 in combination with MD simulations gives in most cases the best agreement with the experimental data. By comparing the emission spectra of 6-N,N-diphenyl-DPPQ with other DPPQ-derivatives one concludes that the molecular fragment diphenyl-amin [(C₆H₅)₂N-] is likely subjected to strong conformational changes in solvents. The large difference between the excited- and state-dipole moments indicates on a strong electron transfer effect being common for all DPPQ derivatives.     

Evaluation of two procedures to determine acid and neutral detergent fibers in ruminant feeds of the temperate region of Argentina

The objective of this work was to compare the traditional Van Soest's procedure to analyze neutral detergent fibers (NDF) and acid detergent fibers (ADF) using filtering crucibles (VS) with a semiautomatic method which uses filter bags in an ANKOM Technology Corp. instrument (ANK). Nine ruminant feeds widely used in the temperate region of Argentina were analyzed: soybean meal expeller, alfalfa, pasture silage, ryegrass, corn silage, weeping lovegrass, tall wheatgrass, guinea grass, and barley grass. Four runs were done for each technique and feed. The comparison of ADF and NDF means by the means test for paired samples showed no significant differences between techniques (alpha = 0.01). The variability among runs was greater with the VS method than the ANK, both for NDF, standard deviation (SD) = 0.71 vs 0.39, and for ADF, SD = 0.83 vs 0.56, but the differences were not significant. The linear regressions were VS = 1.43 + 0.95 ANK; R2 = 0.99, and VS = 0.53 + 0.98 ANK; R2 = 0.99 for NDF and ADF, respectively, which indicated a strong linear relationship among the results of both procedures. It was concluded that the ANK procedure gave results comparable to those of the VS method when ruminant feeds from the temperate region of Argentina were analyzed.     

Investigation of Ring and Star Polymers in Confined Geometries: Theory and Simulations

The calculations of the dimensionless layer monomer density profiles for a dilute solution of phantom ideal ring polymer chains and star polymers with f=4 arms in a Θ -solvent confined in a slit geometry of two parallel walls with repulsive surfaces and for the mixed case of one repulsive and the other inert surface were performed. Furthermore, taking into account the Derjaguin approximation, the dimensionless layer monomer density profiles for phantom ideal ring polymer chains and star polymers immersed in a solution of big colloidal particles with different adsorbing or repelling properties with respect to polymers were calculated. The density-force relation for the above-mentioned cases was analyzed, and the universal amplitude ratio B was obtained. Taking into account the small sphere expansion allowed obtaining the monomer density profiles for a dilute solution of phantom ideal ring polymers immersed in a solution of small spherical particles, or nano-particles of finite size, which are much smaller than the polymer size and the other characteristic mesoscopic length of the system. We performed molecular dynamics simulations of a dilute solution of linear, ring, and star-shaped polymers with N=300 , 300 (360), and 1201 (4 × 300 + 1-star polymer with four arms) beads accordingly. The obtained analytical and numerical results for phantom ring and star polymers are compared with the results for linear polymer chains in confined geometries.