Segmentation of Heteropolymer Sequences Specifying Subsequences with Different Composition and Statistical Properties

We have studied the segmentation of two‐letter AB heterosequences composed of subsequences with different composition and distribution of A and B monomer units along the chain. Our approach is based on the segmentation function S(k) introduced in the present work and on the Jensen–Shannon divergence measure determined with respect to the probabilities of the lengths of uniform blocks of A and B monomer units. It is shown that the function S(k) is extremely sensitive to the sequence statistics. Even visual analysis of S(k) allows judgment on some features of sequence statistics. In particular, function S(k) is constant for random copolymers, it is an oscillating function for random block copolymers and shows monotonic growth up to some constant value for proteinlike copolymers. However, due to significant fluctuations observed for short sequences, the function S(k) can be effectively used only for segmentation of a heterosequence composed of very long subsequences. On the other hand, we find that the Jensen–Shannon divergence measure does not allow one to judge the type of statistics, but is extremely efficient for segmentation of a heterosequence. Therefore, the two introduced functions, being mutually complementary, provide an effective approach for recognizing and segmentation of heterosequences. As an example, the methods developed are applied for concatenating sequences of different proteins.

Segmentation function S(k, l, x) as a function of parameter k and starting number x of “window” for a sequence composed of elastin and ribonuclease sequences.     

Application of Horner–Emmons Olefination to the Crown-Ether Derivatives

An effective synthetic approach to the preparation of a new crown-ether vinylogs involving the Horner–Emmons olefination of carbonyl precursors with the use of C₂- and C₅-phosphonates was proposed. The effects of the conjugation chain length and the nature of the terminal polar functions in the phosphonate reagent on the yield and process stereoselectivity were discussed.     

Substituted and fused spiro[benzo-2-azepine-3,1′-cyclohexanes]

5-Methyl-4,5-dihydro-3H-spiro[benzo-2-azepine-3,1-cyclohexane] N-oxide was rear- ranged into 5-methyl-1-oxo-1,2,4,5-tetrahydro-3H-spiro[benzo-2-azepine-3,1-cyclohexane]. The latter was used for the synthesis of spiro{triazolo[3,4-a]- and-tetrazolo[5,1-a]benzo-2- azepinecyclohexanes}.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1647–1651, August, 2004.     

Nonclassical titanocene silyl hydrides

The titanocene silyl hydride complexes [Ti(Cp)2(PMe3)(H)(SiR3)] [SiR3=SiMePhCl (6), SiPh2Cl (7), SiMeCl2 (8), SiCl3 (9)] were prepared by HSiR3 addition to [Ti(Cp)2(PMe3)2] and were studied by NMR and IR spectroscopy, X-ray diffraction (for 6, 8, and 9), and DFT calculations. Spectroscopic and structural data established that these complexes exhibit nonclassical Ti-H-Si-Cl interligand hypervalent interactions. In particular, the observation of silicon-hydride coupling constants J(Si,H) in 6-9 in the range 22-40 Hz, the signs of which we found to be negative for 8 and 9, is conclusive evidence of the presence of a direct Si-H bond. The analogous reaction of [Ti(Cp)2(PMe3)2] with HSi(OEt)3 does not afford the expected classical silyl hydride complex [Ti(Cp)2(PMe3)(H)[Si(OEt)3]], and instead NMR-silent titanium (apparently TiIII) complex(es) and the silane redistribution product Si(OEt)4 are formed. The structural data and DFT calculations for the compounds [Ti(Cp)2(PMe3)(H)(SiR3)] show that the strength of interligand hypervalent interactions in the chlorosilyl complexes decreases as the number of chloro groups on silicon increases. However, in the absence of an Si-bound electron-withdrawing group trans to the Si-H moiety, a silane sigma complex is formed, characterized by a long Ti-Si bond of 2.658 A and short Si-H contact of 1.840 A in the model complex [Ti(Cp)2(PMe3)(H)(SiMe3)]. Both the silane sigma complexes and silyl hydride complexes with interligand hypervalent interactions exhibit bond paths between the silicon and hydride atoms in Atoms in Molecules (AIM) studies. To date a classical titanocene phosphane silyl hydride complex without any Si-H interaction has not been observed, and therefore titanocene silyl hydrides are, depending on the nature of the R groups on Si, either silane sigma complexes or compounds with an interligand hypervalent interaction.     

Highly accurate evaluation of atomic three-electron integrals of lowest orders

Calculations of three-electron atomic systems in Hylleraas coordinates require integrals involving all the interparticle distances r(ij), which have usually been evaluated by introducing series expansions. For integrals with the smallest powers of r(ij) these expansions do not converge at a satisfactory rate, leading some investigators to introduce convergence-acceleration procedures. This paper recommends the alternative of evaluating these integrals in closed form and presents stable explicit formulas for so doing. Some of the formulas are more compact versions of those in the literature; others have not been previously reported. It is also shown that finite-difference methods can be used with advantage to obtain additional low-order integrals. Sample integral values have been provided for test purposes.     

Nematic ordering in dilute solutions of rodlike polyelectrolytes

Quantitative theory of orientational behavior of rodlike polyelectrolytes in dilute solution is developed. We find that in salt-free solutions many-body Coulomb interactions between macro- and counterions favor nematic ordering. It is shown that the orientationally isotropic phase of the solution becomes unstable toward nematic ordering at polymer concentration smaller than the overlap concentration. Our predictions are consistent with experimental observations for synthetic polyelectrolytes poly(p-phenylene)sulfonates in aqueous solutions.     

Comparative study of photodynamic properties of 13,15-N-cycloimide derivatives of chlorin p6

Comparative study of 13,15-[N-(2-hydroxyethyl)]cycloimide chlorin p6 (2), 13,15-(N-acetoxy)cycloimide chlorin p6 (3), 13,15-(N-hydroxy)cycloimide chlorin p6 methyl ester (4) and 13,15-(N-methoxy)cycloimide chlorin p6 methyl ester (5) together with the previously investigated 13,15-[N-(3-hydroxypropyl)]cycloimide chlorin p6 (1) was performed. The dependence of the key photodynamic properties of 1-5 on the introduced substituents was analyzed. The photoinduced cell-killing activity of 4 is 100- and 280-fold higher than that of chlorin p6 and Photogem, respectively, as estimated on A549 human lung adenocarcinoma cells. The activity is reduced eight times in the order 4 > 5 > 1 > 2 > 3. The intracellular accumulation of 1-5 occurs in cytoplasm in a monomeric form bound to the lipids of cellular membranes. This form of 1, 2, 3, 4 and 5 is characterized by the high quantum yield of singlet oxygen generation, which depends on the introduced substituents, 0.66, 0.59, 0.35, 0.51 and 0.73, respectively. The photostability is two-fold less for 1 and four-fold less for 2, 3 and 5 than for 4. The rates of cellular uptake and efflux of 1-5 vary widely, thus providing the way to optimize the pharmacological properties of the photosensitizer (PS) using the respective substituents. Modifying the substituents, 1-5 were targeted to different cellular organelles. The enhanced accumulation in the Golgi apparatus and mitochondria complemented with diffuse staining of intracellular membranous structures is a property of 1-4. Compound 5 accumulates selectively in the lipid droplets and stains weakly perinuclear structures. Temperature-sensitive mechanisms of transport are responsible for the 1-4 uptake. Diffusion can play a role in the internalization of 5 but not of 1-4. Endocytosis via caveolae, clathrin-dependent and adenosine triphosphate-dependent pathways are not noticeably involved in the 1-5 internalization. Independently from their intracellular localization 1, 4 and 5 are highly efficient near-IR PS, which induce predominantly an apoptotic type of cell death under conditions providing ca 50% level of phototoxicity and necrosis at the 100% level of phototoxicity.     

Biochemical and Structural Studies of Conserved Maf Proteins Revealed Nucleotide Pyrophosphatases with a Preference for Modified Nucleotides

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