A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

Breakage of λ-DNA by inorganic tin and organotin compounds as environmental pollutants

In proportion to the environmental pollution problems caused by organotin compounds, the genotoxicities of tin compounds in the environments have become of interest so as to estimate their safety in recent years. In this work, isolated λ-DNA (double-strand DNA) was incubated with inorganic tin(II) and tin(IV) and five organotin compounds [n-butyltin trichloride, di(n-butyltin) dichloride, methyltin trichloride, dimethyltin dichloride and trimethyltin chloride] in reaction systems both with and without hydrogen peroxide (H₂O₂) content. The tin compounds tested in this study did not induce DNA breakage in the absence of hydrogen peroxide. Divalent inorganic tin (SnCl₂) and tetravalent inorganic tin (SnCl₄) caused DNA breakage in the presence of hydrogen peroxide (10 mM), and the DNA damage activity of inorganic tin was much more potent in divalent inorganic tin (SnCl₂) than in tetravalent inorganic tin (SnCl₄). Divalent inorganic tin (SnCl₂) induced DNA breakage in a concentration-dependent fashion at concentrations greater than 0.1 mM of SnCl₂ in the presence of hydrogen peroxide (10 mM). DNA breakage was not caused by n-butyltin compounds and methyltin compounds either in the presence or in the absence of hydrogen peroxide.     

Organometallic complexes in ascidian embryonic development: II. Effects on different stages and larvae

The effects of the organometallic compounds Bu₂Sn-D -(?;)sorbitol, Bu₂Sn-D -(+)glucose, Bu₂Sn-D -(?)fructose and Bu₂Sn-D -(+)glyceraldehyde were tested in vivo on different stages of Ascidian development, larval movement and metamorphosis. Organotin(IV) complexes are organometallic compounds widely used as industrial biocides, antifouling agents and agricultural fungicides and are toxic to a range of organisms. Two-cell stage embryos, if incubated for one hour in the organotin (IV) solutions, stopped the cleavage, which was restored when they were transferred into normal sea water. The gastrula stage was seriously affected in 10^?4mol dm^?3 solutions of the above-mentioned complexes: 85% of the embryos were anomalous neurulae with open neural folds, 5% were twisted larvae. The gastrulae, when incubated for 1 h in 10^?5mol dm^?3 solutions, developed twisted larvae in ovular envelopes and immobile larvae with twisted tails. Larvae treated with 10^?4mol dm^?3 and 10^?5 mol dm^?3 Bu₂Sn-D -(?)sorbitol, Bu₂Sn-D -(+)glucose and Bu₂Sn-D -(+)glyceraldehyde solutions stopped swimming, did not metamorphose and afterwards underwent cytolysis. An initial hyperactivity of circular movements, followed by immobility, was observed in the larvae incubated in Bu₂Sn-D -(?;)fructose.     

Metal complexation of crosslinked polyacrylamide-supported dithiocarbamates: Effect of the molecular character and extent of crosslinking on complexation

Dithiocarbamate functions were incorporated into different polyacrylamide matrices crosslinked with a flexible and hydrophilic crosslinking agent, tetraethyleneglycol diacrylate (TEGDA), and their complexation behaviours were investigated. Crosslinked polyacrylamides with varying extents of the tetrafunctional TEGDA crosslinks were prepared by free radical solution polymerization at 60°C using potassium persulphate as initiator in ethanol. The dithiocarbamate functionality was incorporated into these polyacrylamides by a two-step polymer-analogous reaction involving (i)trans-amidation with ethylenediamine and (ii) dithiocarbamylation of the aminopolyacrylamide with carbon disulphide and alkali. The complexations of dithiocarbamate with Cu(II), Ni(II), Zn(II), Co(II) and Hg(II) ions were followed under different conditions. The metal ion intake varied with the extent of the crosslinking agent and the observed trend in complexation is Hg(II) > Cu(II)> Zn(II)> Co(II)> Ni (II). The time-course of complexation, the possibility of recycling, swelling characteristics, and spectral and thermal analyses were carried out. The thermal stability increases upon complexation with metal ions.     

Effect of the environment on the stability of surfactant–polypeptide self‐assembled complexes: Molecular dynamics simulations of stoichiometric complexes formed by N‐dodecyltrimethylammonium and poly(α,L‐glutamate) in chloroform,methanol, and water

A series of molecular dynamics simulations have been performed to study the supramolecular structure of self‐assembled complexes formed by N‐dodecyltrimethylammonium cations and the synthetic polypeptide poly(α,L ‐glutamate). The influence of the type of solvent has been investigated, considering explicit environments of chloroform, water, and methanol on a stoichiometric complex containing 15 residues. In chloroform, the complex stabilizes in a regular structure: the polypeptide adopts an α‐helix conformation that is regularly surrounded by surfactant molecules to form electrostatic interactions through a multiple interaction pattern. However, this structure destabilizes in methanol and water: (a) the α‐helix unfolds in the two solvents and (b) the electrostatic links between the surfactant molecules and the polyanion are disrupted in aqueous solution, although these interactions are still preserved in methanol. The role of the solvent environment in stabilizing or destabilizing the polypeptide secondary structure, the organization of the surfactant molecules, and predominantly the surfactant–polypeptide supramolecular organization is discussed in detail. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1122–1133, 2006     

Structural studies on ruthenium(II) complexes used in interphase catalysis for the hydrogenation of ketones

Structural studies were performed on catalytically active ruthenium(II) complexes used in interphases, by means of XAFS spectroscopy. The EXAFS investigations indicate that the complexes retain their structural integrity when they are embedded on polysiloxane matrices to form stationary phase materials. The AXAFS studies reveal that the variations in the catalytic activity of the complexes with different ligands can be correlated to the differences in the electronic structure around the active ruthenium center. The EXAFS investigations show that, in asymmetric transfer hydrogenation reactions catalysed by ruthenium(II) complexes, the co‐catalyst plays a crucial role not only in enhancing the catalytic activity, but also in determining the structure of the intermediate species. Copyright © 2007 John Wiley & Sons, Ltd.     

Antimicorbial effects of newly synthesized organotin(IV) and organolead(IV) derivatives

Triorganotin(IV) and triorganolead(IV) derivatives of the types Me₃Sn(SCZ) and Ph₃Pb(SCZ) (where SCZ^? is the anion of a semicarbanzone ligand) have been synthesized by substitution reactions of trimethyltin chloride and triphenyl-lead chloride with semicarbazones derived from heterocyclic ketones. The resulting complexes have been characterized by elemental analyses, molecualr weight determinations and conductivity measurements. The mode of bonding has been established on the basis of infrared and ¹H, ¹³C and ¹¹⁹Sn NMR spectroscopic studies. Some respresentative complexes have also been evaluated for their antimicrobial effects on different species of pathogenic fungi and bacteria; the results of these investigations have been reported in the present paper.     

Photoelectron spectroscopy of mono and binuclear iron and chromium cyclooctatetraene complexes

The ultraviolet photoelectron spectra of mono and binuclear cyclooctatetraene (COT) complexes (CO)₃FeCOT (I) [(CO)₃Fe]₂COT (II), CpCrCOT (Cp: 1,3 cyclopentadienyl) (III) and (CpCr)₂COT (IV) are reported. The interpretation of the low energy part of the spectra is followed by a discussion concerning the metal–ligand (COT) and metal–metal interactions. The calculated gas phase structure of CpCrCOT is presented and its main features are discussed.     

Experimental and computational studies of intracomplex reactions in Mg+(primary, secondary alkylamine) complexes induced by photoexcitation of Mg+

We report herein a comprehensive study of photoinduced reactions in complexes of Mg+ with primary (n-propyl- and isopropylamine) and secondary amines (dipropyl- and diisopropylamine) in the spectral range of 230-440 nm. Similar to the methyl- and ethylamine complexes studied previously, N-H bond activation of these complexes is very unfavorable. Instead, the C(alpha)-C, C-N, and C(alpha)-H bond-cleavage photoproducts are observed after photoexcitation of the Mg+ complexes (3(2)P<--3(2)S). For Mg+(primary amine) complexes, for example, Mg+-NH2CH2CH2CH3, and Mg+-NH2CH(CH3)2, the photoproducts resulting from C(alpha)--C rupture prevail after P(z) and charge-transfer excitations, whereas the Mg+ photofragment is predominant upon P(x,y) excitation. However, with further N-alkyl substitution, as in Mg+(secondary amine) complexes, for example, Mg+-NH(CH2CH2CH3)2 and Mg+-NH[CH(CH3)2]2, a novel intracomplex C-C coupling photoreaction dominates on P(x,y) excitation of Mg+, which is believed to arise from Mg+* insertion into the C-N bond. With P(z) and charge-transfer excitation, the Mg-R elimination photoproducts, arising from C(alpha)-C bond cleavage, predominate. The energetics and possible mechanisms of the intracomplex photoreactions are analyzed in detail with the help of extensive quantum mechanics calculations.