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.     

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.     

Low-energy ion-assisted control of interfacial structures in metallic multilayers

A molecular dynamics method has been used to simulate the argon ion-assisted deposition of Cu/Co/Cu multilayers and to explore ion beam assistance strategies that can be used during or after the growth of each layer to control interfacial structures. A low-argon ion energy of 5–10 eV was found to minimize a combination of interfacial roughness and interlayer mixing (alloying) during the ion-assisted deposition of multilayers. However, complete flattening with simultaneous ion assistance could not be achieved without some mixing between the layers when a constant ion energy approach was used. It was found that multilayers with lower interfacial roughness and intermixing could be grown either by modulating the ion energy during the growth of each metal layer or by utilizing ion assistance only after the completion of each layers deposition. In these latter approaches, relatively high-energy ions could be used since the interface is buried and less susceptible to intermixing. The interlayer mixing dependence upon the thickness of the over layer has been determined as a function of ion energy.     

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.     

Molecular dynamics studies on octadecylammonium chloride at the air/liquid interface

Molecular dynamics simulations on surfactant octadecylammonium chloride at the air/liquid interface were performed. It was found that the alkyl chains of octadecylammonium would change to order with increasing the concentration of octadecylammonium at the air/liquid interface. Some functions, such as the concentration distributions, the radial distribution function and the mean squared displacement (MSD) were evaluated to investigate the structural properties of interface. We found that the salts can affect octadecylammonium aggregate at the interface: (1) univalent ions, such as chloride and sodium ions, affect slightly the structure of monolayer and (2) bivalent ions, such as sulfate or calcium ions, affect greatly, especially for the bivalent negative ions.     

Chiral separation of 1,1'-bi-2-naphthol and its analogue on molecular imprinting monolithic columns by HPLC

Two molecular imprinting polymer (MIP) monolithic columns with (S)-(-)-1,1'-bi-2-naphthol and (R)-(+)-5,5',6,6',7,7',8,8'-octahydro-1,1'-bi-2-naphthol as the templating molecules, respectively, have been prepared by in situ polymerization using 4-vinylpyridine and ethylene dimethacrylate as functional monomer and cross-linker, respectively. The columns with good flow-through properties were obtained by changing the molar ratio of the functional monomer and the template molecule. The effects of mobile-phase composition on separation of enantiomers were systematically investigated. The results indicate that hydrophobic interaction in aqueous solution and hydrogen-bonding interaction in ACN between the enantiomers and polymers could play important roles in the retention and resolution. The effects of chromatographic conditions, such as flow rate, column temperature, sample loading, on the enantioseparation were also studied. Further, these two MIP columns show a cross-reactivity.