QSAR as a random event: criteria of predictive potential for a chance model

The CORAL software (http://www.insilico.eu/coral) was suggested as a tool to build up quantitative structure–property/activity relationships (QSPRs/QSARs). This software is based on conception “a QSPR/QSAR model should be interpreted as a random event.” This is reflection of fact: different distributions into the training set (substances involved in modeling process) and the validation set (substances, which are not known at the moment of the modeling process) give models with significant dispersion in the statistical quality of the QSPR/QSAR. Results of experiments with the software and possible ways of further improvement of this software are discussed. The most attractive new ways to estimate predictive potential of the CORAL model seem to be the following ones: (i) index of ideality of correlation and (ii) correlation contradiction index. These can be also proposed as criteria of predictive potential for arbitrary QSPR/QSAR.

     

Silyl Modification of Biologically Active Compounds. 10. Lipid Type Organosilicon Derivatives of 8-Hydroxyquinoline and N-(2-Hydroxyethyl)-1,2,3,4-tetrahydro(sila,iso)quinolines

Organosilicon alkylation of the primary alcoholic groups of N-(2-hydroxyalkyl) derivatives of 1,2,3,4-tetrahydroquinoline, tetrahydroisoquinoline, and 4,4-dimethyltetrahydro-4-silaisoquinoline, and also the hydroxyl group of 8-hydroxyquinoline by trialkyl-chloroalkylsilanes under conditions of phase-transfer catalysis has been investigated. The neurotropic properties and acute toxicity of the synthesized compounds have been investigated.__________Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 713–725, May, 2005.     

Alkylation of 2-, 4-, and 8-trialkylsiloxyquinolines by methyl iodide

Trimethyl- and triethylsilyl ethers of 2-, 4-, and 8-hydroxyquinolines have been prepared. The alkylation of these siloxyquinolines by methyl iodide has been studied. In the case of 4-trimethylsiloxyquinoldine, it has been established that both N- and O-alkylation products are formed.Latvian Institute of Organic Chemistry, Riga LV-1006. Translated from Khimiya Geteortsiklicheskikh Soedinenii, No. 9, pp. 1225–1231, September, 1994. Original article submitted September 28, 1994.     

Chain-like assembly of gold nanoparticles on artificial DNA templates via 'click chemistry'

We present a new type of azide-functionalized gold nanoparticle and their coupling to an alkyne-modified DNA duplex using the copper(I)-catalyzed Huisgen cycloaddition ('click chemistry'), resulting in a chain-like assembly of nanoparticles on the DNA template.     

Nanoreactors based on amphiphilic uracilophanes: self-organization and reactivity study

New amphiphilic pyrimidinic macrocycles (APMs) with two (APM-1) and three (APM-2) decyl tails have been synthesized by quaternization of the bridged N. Complex examination of the APM-based systems with the help of tensiometry, conductometry, dynamic light scattering, and UV and NMR spectroscopy provides evidence for their aggregation. Calculations based on surface tension isotherms and on packing parameter considerations make it possible to assume a lamellar packing of macrocycles when aggregating. Marked differences in the aggregation behavior of APM-1 and APM-2 have been found. The additives of polyethylenimine (PEI) exert little influence on the critical micelle concentration (cmc) of APM-1, while in the APM-2/PEI systems there occurs a pronounced decrease in the cmc and also a ca. 2-fold decrease in the surface area per molecule. The APM-based assemblies are explored as nanoreactors for the hydrolysis of O-alkyl O-p-nitrophenyl (chloromethyl)phosphonates (alkyl = ethyl, hexyl). The kinetic study reveals a minor rate effect of the APM-1-based systems. In the APM-2-based systems an acceleration of the hydrolysis of both phosphonates occurs as compared to the uncatalyzed process. Within the APM-2 --> APM-2/PEI --> APM-2/PEI/La(III) series, due to the cooperative contributions of the supramolecular, polymer, and homogeneous catalysis, an increase in the catalytic effect is observed from 30 times to 3 orders of magnitude as compared to that of the basic hydrolysis of the substrates.     

Ion dynamics and water percolation effects in DNA polymorphism

The dynamics of ions and water at the surface of DNA are studied by computer simulations in a wide range of hydrations involving the zone of low-hydration polymorphism in DNA. The long-range mobility of ions exhibits a stepwise increase at three distinct hydration levels. The first of them is close to the midpoint of the water percolation transition as well as the midpoint of the transition between A- and B-DNA forms. It coincides with the onset of the dissociation of ion pairs on the DNA surface probably caused by the increase in the water dielectric permittivity due to the appearance of the spanning hydrogen-bonding network. The other two steps are attributed to the formation of percolating water layers on the surface of DNA accompanied by the progressive escape of ions from the DNA surface. The results agree with earlier experimental data and further corroborate the suggested universal mechanism of the low hydration polymorphism in DNA including intraduplex electrostatic condensation close to the water percolation threshold.     

IR and NMR spectra, intramolecular hydrogen bonding and conformations of mercaptothiacalix[4]arene molecules and their para-tert-butyl-derivative

It is demonstrated that the introduction of p-tert-butyl groups dramatically influences the conformational behaviour of the mercaptothiacalix[4]arene molecules. Quantum-chemical computations in combination with IR and NMR spectroscopy prove that, in contrast to closely related calixarenes, the 1,3-alternate becomes a dominant conformer of p-tert-butyl-mercaptothiacalix[4]arene not only in crystal, but also in solutions and in vacuum. It is shown that the title molecules form essentially non-cooperative intramolecular hydrogen bonds: their SH groups are intramolecularly H-bonded solely to the sulfide groups bridging thiophenolic units. The enthalpy of this bonding, evaluated from Iogansen’s rule, amounts to ca. 1.5 kcal mol⁻¹ per one SH···S bond, which about four times smaller than the enthalpies of cooperative intramolecular H-bonds formed by related calixarenes and thiacalixarenes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On existence of optimal solutions for stochastic differential equations and inclusions with current velocities

For a stochastic differential inclusion given in terms of current velocities (symmetric mean derivatives) on flat n-dimensional torus, we prove the existence of optimal solution minimizing a certain cost criterion. Then this result is applied to the problem of optimal control for equations with current velocities.     

Structural Variability of R2C Adducts of 3a,6a‐Diaza‐1,4‐diphosphapentalene: Tuning the N→P Bonding

3a,6a‐Diaza‐1,4‐diphosphapentalene (DDP) reacts with hexachlorocyclopentadiene to form a stable adduct (ClC)₄C=DDP ( 4 ). The phosphorus atom involved into coordination has a pyramidal arrangement but retains partial double bonding with carbon [1.752(3) Å]. At the same time, the P–N bond remains covalent [1.824(3) Å]. The adduct 4 is better described as a zwitterionic compound with strongly delocalized positive and negative charges. A similar zwitterionic adduct DDP=C(CN)₂ was prepared by the reactions of dichloro‐DDP ( 7 ) with malononitrile in the presence of Et₃N. DFT calculations showed that related structures are formed in the case of the substituents (ClC)₄C=, (HC)₄C=, (NC)₂C=, and (MeCO)₂C=, possessing electron‐delocalizing properties. Compounds with other R₂C groups (R = Ph, Me, C₆F₅, Cl), possessing electronegative properties as well, but insufficient e‐delocalization, demonstrate the noncovalent P–N bonding and a little shorter R₂C–P bond lengths (ca. 1.70 Å).     

Chemical Synthesis of Burkholderia Lipid A Modified with Glycosyl Phosphodiester‐Linked 4‐Amino‐4‐deoxy‐β‐L‐arabinose and Its Immunomodulatory Potential

Modification of the Lipid A phosphates by positively charged appendages is a part of the survival strategy of numerous opportunistic Gram‐negative bacteria. The phosphate groups of the cystic fibrosis adapted Burkholderia Lipid A are abundantly esterified by 4‐amino‐4‐deoxy‐β‐L ‐arabinose (β‐L ‐Ara4N), which imposes resistance to antibiotic treatment and contributes to bacterial virulence. To establish structural features accounting for the unique pro‐inflammatory activity of Burkholderia LPS we have synthesised Lipid A substituted by β‐L ‐Ara4N at the anomeric phosphate and its Ara4N‐free counterpart. The double glycosyl phosphodiester was assembled by triazolyl‐tris‐(pyrrolidinyl)phosphonium‐assisted coupling of the β‐L ‐Ara4N H‐phosphonate to α‐lactol of β(1→6) diglucosamine, pentaacylated with (R)‐(3)‐acyloxyacyl‐ and Alloc‐protected (R)‐(3)‐hydroxyacyl residues. The intermediate 1,1′‐glycosyl‐H‐phosphonate diester was oxidised in anhydrous conditions to provide, after total deprotection, β‐L ‐Ara4N‐substituted Burkholderia Lipid A. The β‐L ‐Ara4N modification significantly enhanced the pro‐inflammatory innate immune signaling of otherwise non‐endotoxic Burkholderia Lipid A.