Theoretical study of cisplatin binding to DNA: the importance of initial complex stabilization

The first and second substitution reactions between activated (hydrolyzed) cisplatin, Pt(NH3)2(H2O)2(2+), and purine bases guanine and adenine are explored using the B3LYP hybrid functional, IEF-PCM solvation models, and large basis sets. The computed free energy barrier for the first substitution is 19.5 kcal/mol for guanine (exptl value = 18.3 kcal/mol) and 24.0 kcal/mol for adenine. The observed predominance toward guanine in the first substitution is explained in terms of significantly larger stabilization energy for the initially formed complex, compared with adenine, in combination with favored kinetics, and represents a revised view of the proposed mechanism for cisplatin binding to DNA. For the second substitution, the computed barrier for Pt(NH3)2G2(2+) head-to-head formation is 22.5 kcal/mol, in very good agreement with experimental data for adduct closure (23.4 kcal/mol). Again, a higher stability in complexation with G over A is ascribed as the main contributing factor favoring G over A substitution. The calculations provide a first explanation for the predominance of 1,2-d(GpG) over 1,2-d(ApG) intrastrand didentate adducts, and the origin of the 5'-3' direction specificity of the 1,2-d(ApG) adducts.     

Changes in mobile phase ion distribution when combining pressurized flow and electric field

The distribution of ions in a capillary with both pressurized flow and an electric field has been studied. We have earlier reported that the overall concentration of ions increase in a capillary with high electric field and a pressurized flow. Now we describe how the ions are distributed in the capillary both along the capillary length and in the radial direction as a result of the parabolic flow profile. We have combined current measurements with finite element techniques in order to get better understanding of the system. We have found that the concentration of the ions that because of the electric mobility moves towards the flow primarily increases at the beginning of the electric field and close to the capillary wall. In view of the results we have proposed an alterative explanation of earlier published results concerning voltage-induced variation in capacity factors.     

Simulation of Industrial Processes Involving Concentrated Aqueous Solutions

The Pitzer model is applied to simulate various single- and multistage modifications of the industrial conversion process

Influence of Diffusion on the Kinetics of an Enzyme-Catalyzed Reaction in Gelatin-Based Gels

The influence of mass-transport limitations on the initial reaction rates of a lipase-catalyzed stereoselective esterification reaction has been investigated for two structurally different gelatin-based gels. The time to reach equilibrium is much longer in pelleted hydrogels (pseudo-solid aqueous gels; PAGs) than in pelleted microemulsion-based gels (MBGs). R/S-(+/-)-2-Octanol and hexanoic acid were used as substrates. The reaction takes place by imbibition of the substrate-containing organic solvent into pores of the pelleted gel. To minimize the diffusion distances, the macroscopic surface areas of the gels were increased by granulating the gel pellets. The experimentally obtained initial reaction rates in granules were in good agreement with the theoretically obtained values from extrapolation to infinitely large areas. However, the still low initial reaction rates in the hydrogels compared to those in microemulsion-based gels cannot be explained by diffusion limitations. This finding was supported by the similar activation energies in both gels in granulated form. Changes in apparent molar standard enthalpy, entropy, and Gibbs energy for the activated complex formation were also estimated. The low reaction rate in hydrogels might thus be due to partial denaturation of the enzyme during the preparation step, to higher surface energy, or to the influence of a different solvent environment on the enzyme in these gels than in the microemulsion-based gels. Copyright 2001 Academic Press.     

Lecture Hall Partitions

We prove a finite version of the well-known theorem that says that the number of partitions of an integer N into distinct parts is equal to the number of partitions of N into odd parts. Our version says that the number of lecture hall partitions of length n of N equals the number of partitions of N into small odd parts: 1,3,5, ldots, 2n-1 . We give two proofs: one via Bott's formula for the Poincaré series of the affine Coxeter group , and one direct proof.     

Time-resolved electrophoretic analysis of mobility shifts for dissociating DNA ligands

Intercalative binding of ligands to DNA can be demonstrated by helix unwinding, monitored by gel electrophoresis of supercoiled DNA, as electrophoretic mobility is sensitive to the topological DNA state. However, we show that an apparent lack of unwinding in an electrophoretic assay could be due to dissociation of the (intercalated) ligand during the analysis, rather than evidence for a nonintercalative mode of binding to DNA. Repetitive scanning during the electrophoresis ensures that release of the ligand during electrophoresis does not affect the measured degree of unwinding, based on the electrophoretic velocity being determined as a function of time. We use this assay to establish intercalation as a mode of binding to DNA for the cyanine dyes YO, YO-PRO as well as two enantiomeric forms of the ruthenium complexes [(phen)2 Ru(tatpp)Ru(phen)2]4+, and to support groove-binding for the new unsymmetrical cyanine dyes BOXTO and BOXTO-PRO. Groove-binding could be concluded from a lack of unwinding, because we could rule out that it is caused by release of the dye during the electrophoresis. The gel electrophoresis has the advantage over hydrodynamic techniques that much smaller sample amounts are required, and our time-resolved approach can be employed in all mobility-shift assays when applied to dissociating complexes.     

A new strategy for the improvement of photophysical properties in ruthenium(II) polypyridyl complexes. Synthesis and photophysical and electrochemical characterization of six mononuclear ruthenium(II) bisterpyridine-type complexes

The synthesis and characterization of six ruthenium(II) bistridentate polypyridyl complexes is described. These were designed on the basis of a new approach to increase the excited-state lifetime of ruthenium(II) bisterpyridine-type complexes. By the use of a bipyridylpyridyl methane ligand in place of terpyridine, the coordination environment of the metal ion becomes nearly octahedral and the rate of deactivation via ligand-field (i.e., metal-centered) states was reduced as shown by temperature-dependent emission lifetime studies. Still, the possibility to make quasi-linear donor-ruthenium-acceptor triads is maintained in the complexes. The most promising complex shows an excited-state lifetime of tau = 15 ns in alcohol solutions at room temperature, which should be compared to a lifetime of tau = 0.25 ns for [Ru(tpy)2]2+. The X-ray structure of the new complex indeed shows a more octahedral geometry than that of [Ru(tpy)2]2+. Most importantly, the high excited-state energy was retained, and thus, so was the potential high reactivity of the excited complex, which has not been the case with previously published strategies based on bistridentate complexes.