Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Structural and magnetic characterization of Mn3IrGe and Mn3Ir(Si1−xGex): experiments and theory

The structural and magnetic properties of a new ternary Ir-Mn-Ge phase, Mn₃IrGe, as well as the solid solution Mn₃Ir(Si_1−xGe_x), 0?x?1, have been investigated by means of X-ray and neutron powder diffraction, magnetization measurements and first principles calculations. The crystal structure is cubic, of the AlAu₄-type (an ordered form of the β-Mn structure), Z=4, space group P2₁3, and the unit-cell dimension varies linearly with the silicon content. For all compositions, antiferromagnetic ordering is found below a critical temperature of about 225 K. The magnetic structure is noncollinear, as a result of frustrated magnetic interactions on a triangular network of Mn atoms, on which the moments rotate 120° around the triangle axes. The magnitude of the magnetic moment at 10 K is 3.39(4) μ_B for Mn₃IrGe. The theoretical calculations reproduce with very good accuracy the magnitudes as well as the directions of the experimentally observed magnetic moments.     

Single crystal Raman study of potassium oxalate monohydrate,K2C2O4. H2O,and potassium oxalate monodeuterate,K2C2O4. D2O

Raman spectra of poly crystalline and single crystal K₂C₂O₄. H₂O and K₂C₂O₄. D₂O have been recorded at room temperature. From an earlier neutron diffraction study it is known that the space group is C⁶₂h. The water molecule occupies a C₂ site and the oxalate ion a C₁ site. The assigned water vibrations show small factor group splitting between g modes (Raman active) and u modes (IR active). The internal oxalate vibrations are found to have wavenumbers in good agreement with those reported from Raman studies of other oxalates.     

Palladium-catalyzed Heck reactions of styrene derivatives and 2-iodo-p-carborane

p-Carborane has been vinylated on the 2-B-atom in high yields using the Heck reaction. Thus, the reaction between 2-iodo-p-carborane and various styrenes [4-H-, 4-C(6)H(4)-, 4-Cl-, 4-Br-, 4-NO(2)-, 4-CH(3)O-, and 4-CH(3)-] resulted in the production of the corresponding trans-beta-(2-B-p-carboranyl)styrene in DMF solution when reacted in the presence of silver phosphate and the palladacycle Herrmann's catalyst.     

Stereoselectivity and competing reactions as studied by lipase-catalyzed esterifications in aqueous lecithin-based gelatin gels

 The enzyme catalyzed conversion of R/S-(±)-2-octanol with hexanoic acid to R/S-(±)-2-octyl hexanoate has been studied in different microenvironments and in the presence of the competing substrate ethanol. The reactions were performed in various gels made from aqueous gelatin solutions and liposome dispersions or isotropic liquid solutions, with or without oil and ethanol. The lipase Candida sp. (SP 525) was dissolved in the dispersions or solutions stabilized by the naturally occurring zwitterionic surfactant soybean lecithin. The sectioned porous gel was immersed in hexane containing 0.33 mol dm^-3 of racemic 2-octanol and hexanoic acid. Since ethanol acts both as a substrate and as a part of the gel it is of fundamental interest to know the phase behaviour of the used systems. Partial phase diagrams for the systems ethanol–water–soybean lecithin and ethanol/water (7:3)–oil–soybean lecithin were determined at 298.2 K. The oil was either castor oil or hexadecane. The conversion of R-2-octyl hexanoate was about 0.45 when no or small amounts of ethanol was present, but decreased considerably with high amounts of ethanol present and ethyl hexanoate became the main product. Hydrolysis of R-2-octyl hexanoate was favoured in the latter systems and hexanoic acid formed was immediately esterified to ethyl hexanoate. The conversion of R-2-octyl hexanoate and ethyl hexanoate depends only on the ethanol content present in the systems and is thus independent of the environment of the enzyme. However, the chiral esters synthesized from racemic 2-octanol and hexanoic acid showed high optical purities regardless of the ethanol content. Received: 1 July 1996 Accepted: 30 August 1996     

Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine

DNA-protein cross-linking is one of the many DNA lesions mediated by hydroxyl radicals, the most damaging among the reactive oxygen species in biological systems. Density functional theory methods are employed to investigate the complex reaction mechanisms of the formation of cytosine-tyrosine cross-links as observed in gamma-irradiated aqueous solutions of cytosine and tyrosine, as well as in gamma-irradiated nucleohistone. The majority of the radical addition mechanisms considered are found to have significant barriers and therefore to be thermodynamically unfavorable for the formation of the initial cross-linked product. Our calculated reaction potential energy surfaces suggest that a feasible complete mechanism consists of radical combination forming the initial cross-linked product, a hydrogen shuffle within the initial cross-linked product, and an acid-catalyzed dehydration reaction. Water and hydrogen-bonding interactions are suggested to play a key role in catalyzing the hydrogen-transfer step of the reaction.