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Modeling of interface phenomena in liquid under vibration, using the chemical model.

An analysis of interface phenomena in a liquid under a vibration field is presented, based on the chemical model of vibration in a liquid. The objects studied are a bubble, a solid surface, and a linear macromolecule, in a vibrated liquid. It is concluded that many sonochemical phenomena can be realized in some different (two or more) mechanisms, and mutually stimulate. Inharmonic effects and the influence of distant neighbors are analyzed.

Journal Article↗

Quantum chemical modeling of through-hydrogen bond spin-spin coupling in amides and ubiquitin.

Through-hydrogen bond spin-spin coupling has been investigated computationally in the formamide dimer and in fragments of the protein ubiquitin. The Fermi-contact term was calculated by finite perturbation theory with the B3LYP DFT method with several basis sets. The distance and angular dependence of the 3J(N,C') coupling constant (N-H--O=C) in the hydrogen-bonded formamide dimer was firstly examined for a wide range of mutual arrangements, also in relation to the stability of the dimer. The magnitude of 3J(N,C') is relatively insensitive to the dihedral angle between the two amide planes, whereas values between 1-2 Hz are calculated for a variety of arrangements, including non-linear hydrogen bonds, in agreement with the shape of some occupied, low-lying molecular orbitals which connect donor and acceptor. Then, fragments of the ubiquitin protein (for which such coupling constants are experimentally available) were generated by removing from the experimental structure all amino acids except those involved in hydrogen bonding, and coupling constants were calculated for such fragments. Although calculated 3J(N,C') values are sometimes overestimated, they generally correlate with the corresponding experimental values.

Amides↗

Quantum chemical modeling of the reduction of cis-diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anion.

We present here both an ab initio and quantum mechanical/molecular mechanical (QM/MM) study of the cis-[Pt(NH3)2Cl4] complex reduction by methyl thiolate anion, SCH(-3), which is used as a model of glutathione. Geometry and electronic structure of cis-[Pt(NH3)2Cl4] are determined without and in aqueous medium. The mechanism of the reaction of reduction is characterized. The calculated activation energy of the reaction compares remarkably well with the experimental value.

Antineoplastic Agents↗

Physico-chemical modeling of the role of free radicals in photodynamic therapy. IV. Quantitative aspects of photodynamic effects on free radicals generated in cell cultures.

Production and the mechanism of the interactions of free radicals generated by stimulated macrophages in the presence of luminol and a free radical inhibitor was investigated to determine the possibility of using luminol-dependent chemiluminescence for studying photodynamic effects in biology. Earlier measurements have been revisited and additional experiments performed indicating that oxidation products of luminol neither inhibit the in vitro formation of radicals nor quench CL. Simulation based on the mechanism suggested revealed that the likely value for the rate constant of the primary step between luminol and superoxide anion radicals producing luminol radicals is 5x10(2)-1x10(3) M-1s-1. It has been established that the ratio of the concentration of radicals generated by the biological system to that formed by oxidation of luminol exceeds 10(3); that is, the contribution of the latter is negligible and the system is appropriate to measure quantitatively the effect of excited photosensitizers on free radicals.

Animals↗

Could the tyrosine-histidine ligand to CuB in cytochrome c oxidase be coordinatively labile? Implications from a quantum chemical model study of histidine substitutional lability and the effects of the covalent tyrosine-histidine cross-link.

Density functional theory calculations have been used to evaluate the effects of inter-ring interactions within a covalently linked histidine-tyrosine cofactor such as that which is a ligand to the Cu(B) centre in cytochrome c oxidases and to investigate the energetics of histidine substitution at the Cu(B) centre. Small, but significant, perturbations of the redox potentials and/or p K(a) values of the histidine imidazole, the tyrosine phenol and the copper ion are found. The Cu(B)-N(cofactor) bond is estimated to be weaker than the Cu(B)-N(histidine coligand) bonds in the Cu(B)(I) state and in the Cu(B) (II) state when the cofactor is oxidized, by approximately 13 kJ/mol and approximately 23 kJ/mol, respectively. The calculations reveal that displacement of a histidine ligand from the Cu(B) centre, as is suggested in proposals of "histidine cycle" mechanisms for proton pumping in cytochrome c oxidases, is only energetically feasible if accompanied by protonation of the histidine imidazole and coupled to an endothermic process. It is proposed that the histidine-tyrosine cofactor ought to be considered as the substitutionally labile ligand to Cu(B) as the covalent crosslink would ensure displacement of the cofactor from Cu(B)-driven helix deformation. It is estimated that this process could store up to approximately 70 kJ/mol, which, based upon thermodynamic considerations, is sufficient for the pumping of two protons in the later steps (reductive phase) of the catalytic cycle. Ramifications of this proposition for the mechanism of proton pumping in cytochrome c oxidases are discussed.

Amino Acid Substitution↗

Physico-chemical model for DNA alkaline elution: new experimental evidence and differential role of DNA length, chain flexibility and superpacking.

For a better understanding of data provided by DNA alkaline elution technique, a new analytical model has been developed which takes into consideration both the physicochemical properties of in situ DNA strand (length and flexibility/superpacking) and the geometric and hydrodynamic configuration of the elution apparatus (flow and filter conditions). Simulation by this model of experimental data previously obtained before and after carcinogens administration, has shown that for constant flow and filter conditions elution profiles are dependent, not only from DNA molecular weight, but also from a parameter critically related to modifications in chain flexibility/superpacking. This has been confirmed by several independent observations, including the time-dependent changes in non-denaturing lysing solution monitored by hydroxylapatite and alkaline elution techniques.

Animals↗

Dioxygenases without requirement for cofactors and their chemical model reaction: compulsory order ternary complex mechanism of 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase involving general base catalysis by histidine 251 and single-electron oxidation of the substrate dianion.

1H-3-Hydroxy-4-oxoquinaldine 2,4-dioxygenase (Hod) is a cofactor-less dioxygenase belonging to the alpha/beta hydrolase fold family, catalyzing the cleavage of 1H-3-hydroxy-4-oxoquinaldine (I) and 1H-3-hydroxy-4-oxoquinoline (II) to N-acetyl- and N-formylanthranilate, respectively, and carbon monoxide. Bisubstrate steady-state kinetics and product inhibition patterns of HodC, the C69A protein variant of Hod, suggested a compulsory-order ternary-complex mechanism, in which binding of the organic substrate precedes dioxygen binding, and carbon monoxide is released first. The specificity constants, k(cat)/K(m,A) and k(cat)/K(m,O)()2, were 1.4 x 10(8) and 3.0 x 10(5) M(-1) s(-1) with I and 1.2 x 10(5) and 0.41 x 10(5) M(-1) s(-1) with II, respectively. Whereas HodC catalyzes formation of the dianion of its organic substrate prior to dioxygen binding, HodC-H251A does not, suggesting that H251, which aligns with the histidine of the catalytic triad of the alpha/beta hydrolases, acts as general base in catalysis. Investigation of base-catalyzed dioxygenolysis of I by electron paramagnetic resonance (EPR) spectroscopy revealed formation of a resonance-stabilized radical upon exposure to dioxygen. Since in D(2)O spectral properties are not affected, exchangeable protons are not involved, confirming that the dianion is the reactive intermediate that undergoes single-electron oxidation. We suggest that in the ternary complex of the enzyme, direct single-electron transfer from the substrate dianion to dioxygen may occur, resulting in a radical pair. Based on the estimated spin distribution within the radical anion (observed in the model reaction of I), radical recombination may produce a C4- or C2-hydroperoxy(di)anion. Subsequent intramolecular attack would result in the 2,4-endoperoxy (di)anion that may collapse to the reaction products.

Alanine↗

Ring scission of diastereomeric 4-butylspiropentylcarbinyl radicals as a chemical model for identifying enzyme-catalyzed FAD adducts resulting from spiropentylacetyl-CoA.

Both diastereomeric 4-butylspiropentylcarbinyl bromides (14a and 14b) were synthesized in seven steps starting from 1-heptyne, and the stereochemical assignments based upon NOE experiments were confirmed by converting their immediate alcohol precursors (13a and 13b) to 1,4-dibutylspiropentanes (17a and 17b) with C(1) and C(2) symmetry. Each bromide was used to generate its corresponding spiropentylcarbinyl radical (18a and 18b) via its AIBN-initiated tri-n-butyltin hydride reduction. The radical-trapped products are identified, the preferred ring scission mode is identified (C1[bond] C2 bond cleavage), and the estimated rates for the ring opening of 4-butylspiropentylcarbinyl radical (18, k(25) degrees C > or = approximately 5 x 10(9) s(-1)) and 2-butyl-1-vinylcyclopropylcarbinyl radical (33, k(25) degrees C approximately 5 x 10(8) s(-1)) are reported. High-level ab initio calculations addressing the ring-opening isomerizations of cyclopropylcarbinyl and spiropentylcarbinyl radicals also are presented. These results in conjunction with a previous study enable us to propose two structures for the enzyme-catalyzed FAD adducts resulting from spiropentylacetic acid-CoA, a synthetic byproduct of fatty acid metabolism.

Coenzyme A↗