Modeling of recombination kinetics of radical pairs in magnetic field. Comparison with experimental dependences on the frequency of encounters in biradicals

The recombination kinetics of spin-correlated radical pairs (RPs) with three nonequivalent magnetic nuclei were calculated under conditions of enforced encounters between radicals at time-independent frequency n_dif. The simplest two-position model of a RP was used, which includes two states (contact state and distance-separated state) of the RP, differing in magnitude of isotropic spin-spin exchange interaction between radicals. The calculated kinetic curves were treated in terms of a three-exponential model. The dependences of corresponding rate constants (k _rec) on n_dif, external magnetic field strength (B ₀), and intensity, A _eff, of isotropic hyperfine coupling (HFC) were obtained. The k _rec-vs.-n_dif or k _rec-vs.-viscosity (n_dif varies simultaneously with the inverse lifetime of the contact state) plots pass through maxima whose positions are shifted from the n_dif region near the A _eff value at B ₀ = 0.5 G toward high n_dif values with an increase in B ₀. At n_dif ≫ A _eff, the k _rec-vs.-B ₀ plots pass through maxima in the region B ₀ = A _eff. The calculated dependences are compared with experimental data on recombination of biradicals. The results of calculations show that the experimentally observed maxima on the k _rec-vs.-B ₀ or k _rec-vs.-n_dif plots can be due to peculiar features of the spin dynamics induced by the hyperfine coupling rather than the exchange interaction effects, as is commonly accepted. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1103–1110, May, 2005.     

Kinetic studies of some substituted hexarhodium carbonyl clusters

Reactions of the halides X- (X- = chloride, bromide or iodide) with the substituted cluster Rh6(CO)15(PPh3) in oxygen-free chloroform lead to [Rh5(CO)14(PPh3)]-, Rh(CO)2(PPh3)2X and [Rh(CO)2X2]- in the molar ratios 2:1: approximately 13. Oxidation by the solvent is assumed to lead to most of the Rh(I) product, and the stoichiometry for reactions with I- can be defined as 4Rh6(CO)15(PPh3) + 27I- + 12CHCl3 --> 2[Rh5(CO)14(PPh3)]- + Rh(CO)2(PPh3)2I + 13[Rh(CO)2I2]- + 6C2H2Cl4 + 4CO + 12Cl-. This can be rationalized quite simply with the aid of a few generally justifiable assumptions. Rate constants for reactions with bromide increase to a limiting value with increasing [Br-] in a way that shows that breaking of one Rh-Rh bond, with an unusual closo to nido structural change, is rate determining. This opening of the cluster might be spontaneous or solvent induced. To complete the reaction, the bromide has to compete with the reverse nido to closo change. The same closo to nido change is also a major rate determining step for reactions with P(OPh)3 in oxygen-free solutions, and for reactions with bromide in oxygenated solutions in the presence of trifluoroacetic and some other acids. The limiting rates increase slightly with increasing basicity of the ligands P(p-XC6H4)3 along the series X = F3C, Cl, F, H and MeO. Activation parameters for these reactions are reported.     

Conformational analysis of oligosaccharides in solution

A complete understanding of the role of carbohydrates in biological systems is to a large extent dependent on the information available about the equilibrium mixture and about the preferred conformation of the carbohydrate molecules in solution. The conformational analysis offers a tool which can determine all possible conformations which influence the solution behavior of carbohydrates. This paper attempts to survey the progress in the theoretical conformational analysis of saccharides in solution. The conformational analysis will be discussed in detail both with respect to the strategy for the investigation of conformational properties but also with regard to the quality of the method used for calculations of the energy of the isolated molecule and free energy of solvation. Finally, examples will be given to illustrate how the methods of conformational analysis can be used to estimate the solution behavior of cyclic model compounds of carbohydrates 2-methoxytetrahydropyran, monosaccharide D -glucopyranose, and two disaccharides; β-maltose and β-cellobiose.     

Addition of nitriles to alkaline earth metal complexes of 1,2-bis[(phenyl)imino]acenaphthenes

Compounds [Sr(dpp-bian)(thf)4] (2), [Ba(dpp-bian)(dme)2.5] (3) and [Mg(dtb-bian)(thf)2] (4) (dpp-bian = 1,2-bis[(2,6-diisopropylphenyl)imino]acenaphthene; dtb-bian = 1,2-bis[(2,5-di-tert-butylphenyl)imino]acenaphthene) were prepared by reduction of dpp-bian and dtb-bian with an excess of metallic Mg, Sr, or Ba in THF or DME. Reactions of [Mg(dpp-bian)(thf)3], 3, and 4 with diphenylacetonitrile gave keteniminates [Mg(dpp-bianH)(NCCPh2)(thf)2] (5), [Mg(dtb-bianH)(NCCPh2)(thf)2] (6), and [Ba(dpp-bianH)(NCCPh2)(dme)2] (7), respectively. The reaction of 2 with CH3C[triple chemical bond]N in THF gave [{Sr(dpp-bianH)[N(H)C(CH3)C(H)CN](thf)}2] (8). The compounds 2, 3, 5-8 were characterized by elemental analysis, and IR and NMR spectroscopy. Molecular structures of 2, 3, 7, and 8 were determined by single-crystal X-ray diffraction. In contrast to reactions of alkali-metal reagents, magnesium amides, or yttriumalkyls with alpha-H acidic nitriles, which are accompanied by an amine or an alkane elimination, the reactions of [Mg(dpp-bian)(thf)3] (1), 2, 3, and 4 with such nitriles proceeded with formation of Mg, Sr, and Ba keteniminates and simultaneous protonation of one nitrogen atom of the bian ligand. The NMR spectroscopic data obtained for complex 5 indicated that in solution the amino hydrogen atom underwent the fast (on the NMR timescale) shuttle transfer between both nitrogen atoms of the dpp-bianH ligand.     

2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides: synthesis,stereospecificity, some chemical transformations,and conformational analysis

The synthesis of methyl 5-O-benzoyl-2-chloro-2,3-dideoxy-3-fluoro-beta-d-ribofuranoside (5) and its use as a glycosylating agent for persilylated thymine, N(6)-benzoyladenine, and N(4)-benzoylcytosine are described (Scheme 1). The 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides 10-12 synthesized were transformed to 2',3'-dideoxy-3'-fluoro-alpha- and -beta-d-erythro-pentofuranoside nucleosides of thymine (13a,b), adenine (14a,b), and cytidine (15a,b) by treatment with tributyltin hydride in the presence of alpha,alpha'-azobisisobutyronitrile (Scheme 2). Treatment of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides with 1 M MeONa/MeOH under reflux for 1-5 h afforded 2',3'-didehydro-2',3'-dideoxy-2'-chloro-d-pentofuranosyl nucleosides as the principal products (47-81%) of the reaction, along with recovered starting nucleoside (11-33%) (Scheme 3). Easy HF elimination was also observed in the case of the 2'-azido-2',3'-dideoxy-3'-fluoro-beta-d-ribofuranosides of thymine (17) and adenine (20) (Scheme 3). The role of conformational peculiarities of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides as well as of 17 and 20 in the observed exclusive elimination of HF is discussed. The conformational analysis of a rather broad palette of 2,3-dideoxy-3-fluoro-2-(X-substituted)-d-ribofuranosides was performed with the aid of the PSEUROT (version 6.3) program, using (i) the recently reparametrized Karplus-type relation (Chattopadhyaya and co-workers. J. Org. Chem. 1998, 63, 4967) and (ii) empirical bond angle correction terms suggested by us. The predictive power of the Brunck and Weinhold model (J. Am. Chem. Soc. 1979, 101, 1700) of the gauche effect between atoms and groups as a conformational driving force acting upon the pentofuranose ring is explored. Their model invokes maximum antiperiplanar sigma <--> sigma stabilization when the donating bond is the least polar one and the acceptor orbital is at the most polarized bond and is found at least as satisfactory, and in various specific cases more so than, as rationalizations on the basis of the preference of the gauche vs the trans conformation of two vicinal electronegative substituents (Wolfe. Acc. Chem. Res. 1972, 5, 102).     

Distance dependence of electron transfer in rigid,cofacially compressed,pi-stacked porphyrin-bridge-quinone systems

The electron-transfer (ET) dynamics of a series of unusually rigid pi-stacked porphyrin-quinone (P-Q) systems, in which sub-van der Waals interplanar distances separate juxtaposed porphyryl, aromatic bridge, and quinonyl components of these assemblies, are reported. The photoinduced charge separation (CS) and thermal charge recombination (CR) ET reactions of [5-[8'-(2',5'-benzoquinonyl)-1'-naphthyl]-10,20-diphenylporphinato]zinc(II) (1a-Zn), [5-[8'-(4'-[8'"-(2'"',5'"'-benzoquinonyl)-1'"-naphthyl]-1'-phenyl)-1'-naphthyl]-10,20-diphenylporphinato]zinc(II) (2a-Zn), and [5-(8'-[4'-(8'"-[4'"'-(8'"-[2'"',5'"'-benzoquinonyl]-1'"-naphthyl)-1'"'-phenyl]-1'"-naphthyl)-1'-phenyl]-1'-naphthyl)-10,20-diphenylporphinato]zinc(II) (3a-Zn) in CH(2)Cl(2) were investigated by pump-probe transient absorption spectroscopy. Analyses of these data show that the phenomenological ET distance dependence (beta) for both the CS and CR reactions in these systems is soft (beta(CS) = 0.43 A(-1); beta(CR) = 0.35 +/- 0.16 A(-1)). This work demonstrates that simple aromatic building blocks such as benzene, which are characterized by highly stabilized filled molecular orbitals and large HOMO-LUMO gaps, can provide substantial D-A electronic coupling when organized within a pi-stacked structural motif that features a modest degree of arene-arene interplanar compression.     

DNA Effect on Cis–Trans Equilibrium and Fluorescent Properties of 3,3′-Diethyl-9-thiomethylthiacarbocyanine Iodide in Aqueous Solution

The influence of DNA on the cis–trans equilibrium and fluorescent properties of 3,3-diethyl-9-thiomethylthiacarbocyanine iodide (DTTC) in a phosphate buffer (pH 7) was studied by various photochemical techniques. The interaction of dye molecules with DNA leads to the formation of stable noncovalently bonded complexes. Data obtained from DTTC absorption and fluorescence spectra suggest that complexation proceeds primarily through the cis-form of the dye. Complexation with DNA leads to a substantial increase in the quantum yield of the triplet state of DTTC molecules. The rate constant for quenching the dye triplet state by oxygen turned out to be significantly lower than the diffusion-controlled value.     

Primate beta-defensins--structure, function and evolution

Host defense peptides (HDPs) are endogenous antibiotics that play a multifunctional role in the innate immunity of mammals. Among these, beta-defensins contribute to mucosal and epithelial defense, also acting as signal molecules for cellular components of innate and adaptive immunity. Numerous members of this family have been identified in mammalian and avian species, and genomic studies in human and mouse indicate a considerable complexity in their gene organization. Recent reports on the evolution of primate and rodent members of this family indicate quite a complex pattern of variation. In this review we briefly discuss the evolution of mammalian beta-defensins in relation to other types of defensins, and then concentrate on the evolution of beta-defensins 1 to 4 in primates. In particular, the surprisingly varied patterns of evolution, which range from neutral or weakly purifying, to positive selection to a high level of conservation are analyzed in terms of possible genetics, structural or functional implications, as well as to observed variations on the antimicrobial activity in vitro. The role of polymorphisms in the genes encoding for these host defense peptides in determining susceptibility to human diseases are also briefly considered.     

Bismuth-catalyzed benzylic oxidations with tert-butyl hydroperoxide

[reaction: see text] Oxidation of alkyl and cycloalkyl arenes with tert-butyl hydroperoxide catalyzed by bismuth and picolinic acid in pyridine and acetic acid gave the corresponding benzylic ketones (48-99%). Alternatively, oxidation of methyl arenes gave the corresponding substituted benzoic acids (50-95%). Preliminary mechanistic studies were consistent with a radical mechanism rather than a bismuth(III)-bismuth(V) cycle.     

Self-assembled luminescent CdSe-ZnS quantum dot bioconjugates prepared using engineered poly-histidine terminated proteins

We report a simple and versatile approach for the conjugation of luminescent CdSe-ZnS core-shell quantum dots (QDs) to proteins through coordination of engineered C-terminal oligohistidine sequences. Several histidine tail containing proteins were self-assembled onto the QD surface using this method. A recombinant antibody specific for the high explosive 2,4,6-trinitrotoluene (TNT) was conjugated to QDs through a carboxy terminal histidine tail and the bioconjugate used to detect TNT by competitive immunoassay. TNT was detected over the range of 10 μg/ml down to 41 ng/ml using the scFv conjugated to QDs. These results open up the possibility to conjugate luminescent QDs to a whole range of proteins to form QD bioconjugates that can be effectively used in bio-oriented applications, such as sensing, imaging, immunoassay and other diagnostics.