Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism

5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of approximately 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be approximately 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.     

Automatic fitting procedures for EPR spectra of disordered systems: matrix diagonalization and perturbation methods applied to fluorocarbon radicals

Two types of automatic fitting procedures for EPR spectra of disordered systems have been developed, one based on matrix diagonalization of a general spin Hamiltonian, the other on 2nd order perturbation theory. The first program is based on a previous Fortran code complemented with a newly written interface in Java to provide user-friendly in and output. The second is intended for the special case of free radicals with several relatively weakly interacting nuclei, in which case the general method becomes slow. A least squares' fitting procedure utilizing analytical or numerical derivatives of the theoretically calculated spectrum with respect to the g- and hyperfine structure (hfs) tensors was used to refine those parameters in both cases. 'Rigid limit' ESR spectra from radicals in organic matrices and in polymers, previously studied experimentally at low temperature, were analyzed by both methods. Fluorocarbon anion radicals could be simulated, quite accurately with the exact method, whereas automatic fitting on, e.g. the c-C(4)F(8)(-) anion radical is only feasible with the 2nd order approximative treatment. Initial values for the (19)F hfs tensors estimated by DFT calculations were quite close to the final. For neutral radicals of the type XCF(2)CF(2)* the refinement of the hfs tensors by the exact method worked better than the approximate. The reasons are discussed. The ability of the fitting procedures to recover the correct magnetic parameters of disordered systems was investigated by fittings to synthetic spectra with known hfs tensors. The exact and the approximate methods are concluded to be complementary, one being general, but limited to relatively small systems, the other being a special treatment, suited for S=1/2 systems with several moderately large hfs.     

Pd-catalyzed diarylation of aniline--a way to a non-linear bis(terpyridyl) ligand providing increased electronic communication

An amine-linked bis(terpyridyl) ligand, prepared via Pd-catalyzed diarylation of aniline, mediates unusually strong metal-metal interaction in its Ru(2) polypyridyl complex.     

Atom detection and photon production in a scalable, open, optical microcavity

A microfabricated Fabry-Perot optical resonator has been used for atom detection and photon production with less than 1 atom on average in the cavity mode. Our cavity design combines the intrinsic scalability of microfabrication processes with direct coupling of the cavity field to single-mode optical waveguides or fibers. The presence of the atom is seen through changes in both the intensity and the noise characteristics of probe light reflected from the cavity input mirror. An excitation laser passing transversely through the cavity triggers photon emission into the cavity mode and hence into the single-mode fiber. These are first steps toward building an optical microcavity network on an atom chip for applications in quantum information processing.     

Binding of intercalating and groove-binding cyanine dyes to bacteriophage t5

The interaction between four related cyanine dyes and bacteriophage T5 is investigated with fluorescence and absorption spectroscopy. The dyes, which differ in size, charge, and mode of DNA-binding, penetrate the capsid and bind the DNA inside. The rate of association decreases progressively with increasing dye size, from a few minutes for YO to more than 50 h for YOYO (at 37 degrees C). The relative affinity for the phage DNA is a factor of about 0.2 lower than for the same T5-DNA when free in solution. Comparison of groove-bound BOXTO-PRO and intercalating YO-PRO shows that the reduced affinity is not due to DNA extension but perhaps influenced by competition with other cationic DNA-binding agents inside the capsid. Although, the extent of dye binding to the phages decreases with increasing external ionic strength, the affinity relative to free DNA increases, which indicates a comparatively weak screening of electrostatic interactions inside the phage. The rate of binding increases with increasing ionic strength, reflecting an increase in effective pore size of the capsid as electrostatic interactions are screened and/or a faster diffusion of the dye through the DNA matrix inside the capsid as the DNA affinity is reduced. A combination of electron microscopy, light scattering, and linear dichroism show that the phages are intact after YO-PRO binding, whereas a small degree of capsid rupture cannot be excluded with BOXTO-PRO.     

Effects of OH radical addition on proton transfer in the guanine-cytosine base pair

Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.     

Theoretical study of ibuprofen phototoxicity

The photochemical properties and degradation of the common nonsteroid anti-inflammatory drug ibuprofen is studied by means of hybrid density functional theory. Computed energies and properties of various species show that the deprotonated form dominates at physiological pH, and that the species will not be able to decarboxylate from a singlet excited state. Instead, decarboxylation will occur, with very high efficiency, provided the deprotonated compound can undergo intersystem crossing from an excited singlet to its excited triplet state. In the triplet state, the C-C bond connecting the carboxyl group is elongated, and the CO2 moiety detaches with a free energy barrier of less than 0.5 kcal/mol. Depending on the local environment, the decarboxylated product can then either be quenched through intersystem crossing (involving the possible formation of singlet oxygen) and protonation, or serve as an efficient source for superoxide anions and the formation of a peroxyl radical that will initiate lipid peroxidation.     

Recent advances with TLR2-targeting lipopeptide-based vaccines

The next generation of vaccines are being rationally designed according to rules that govern the way in which antigen is recognised by and stimulates the immune system. Amongst the first cells that encounter potentially dangerous agents such as viruses and bacteria are cells of the innate immune system, such as dendritic cells, that are widely distributed throughout the body including the skin. These cells patrol most tissues and have on their surface an array of receptors that have evolved to recognise many of the surface features of pathogens including the lipids and carbohydrates of structural lipoproteins, glycolipids and glycoproteins. Once encountered, recognised and engaged by a particular receptor on the dendritic cell, pathogenic material may then be transported inside the cell and processed for presentation to cells of the adaptive immune system. The result of this concert of events is a specific cellular or antibody response to particular epitopes of the invading pathogen. If then ways can be found to specifically target dendritic cells, through their specific receptors, then the efficacy and potency of vaccines could well be greatly improved. This review covers some of the approaches that we and others are pursuing in order to achieve this result.