New efficient total syntheses of derivatives of protoporphyrin-IX bearing deuteriated methyl groups

New total syntheses of hemins which are regioselectively deuteriated in the 1,5 (2), 5 (3) or 8 (4) methyl groups are described. Syntheses of hemins 2 and 3 follow the progression from pyrromethane 12 to t-butyl tripyrrene-carboxylate hydrobromide (17 and 30) and then to a,c-biladiene dihydrobromide (19 and 31), but for reasons of economy in use of labeled monopyrroles, the o,c-biladiene dihydrobromide 40 for hemin 4 is approached in an initially “clockwise” manner by synthesis of a benzyl tripyrrene-carboxylate hydrobromide 37 from the pyrromethane 5. Cyclization of the a,c-biladienes (19, 31, and 40) was accomplished by brief heating in dimethylformamide in the presence of copper(II) chloride.     

SEARCH FOR SINGLET OXYGEN LUMINESCENCE IN THE DISPROPORTIONATION OF HO2/O2

Abstract— During the reaction HO₂+ HO₂ (or O₂^-) = H₂O₂+ O₂ in aqueous solution, no luminescence in the region 620–720 nm, expected if the product O₂ were formed in a singlet state, could be detected. If any singlet O₂ is formed, its yield must be less than 10%. Faint luminescence, sometimes found at shorter wavelengths, was shown to arise from reaction of HO₂ with impurities in the reagents present.     

A theoretical study of electronic and vibrational properties of neutral,cationic, and anionic B24 clusters

The equilibrium geometries, electronic and vibrational properties, and static polarizability of B₂₄, B, and B clusters are reported here. First‐principles calculations based on density functional theory predict the staggered double‐ring configuration to be the ground state for B₂₄, B, and B, in contrast to the quasi‐planar structure observed in small neutral and ionized B_n clusters with n ≤ 15. Furthermore, the (4 × B₆) tubular structure is found to be relatively stable in comparison to the 3D cage structure. The presence of delocalized π and multicentered σ bonds appears to be the cause of the stability of the double‐ring and tubular isomers. For the ground state of B₂₄, the lower and upper bound of the electron affinity is 2.67 and 2.81 eV, respectively, and the vertical ionization potential is 6.88 eV. Analysis of the frequency spectrum of the double‐ring and tubular isomers reveals the characteristic vibrational modes typically observed in carbon nanotubes. The corresponding IR spectrum also reflects the presence of some of these characteristic modes in the neutral and ionized B₂₄, suggesting that double‐ring and tubular structures can be considered as the building blocks of boron nanotubes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

DISTRIBUTION AND ELIMINATION OF PHOTOFRIN II IN MICE

The distribution and elimination of [14C]PII, the radioisotopically-labeled equivalent of the mixture of porphyrins known as Photofrin II used in the photodynamic treatment of solid tumors, were determined in tumor-free and SMT-F tumor-bearing DBA/2 Ha-DD mice. Following i.p. injection, drug was absorbed from the peritoneum with a half-life of about 1 h; elimination from plasma was rapid, declining about 1.4 logs in concentration over 48 h following i.v. administration. However, some [14C]-activity was still detectable after 75 days. Normal tissues take up the drug within about 7.5 h after administration, with peak concentrations distributed as follows: liver, adrenal gland, urinary bladder greater than pancreas, kidney, spleen greater than stomach, bone, lung, heart greater than muscle much greater than brain. Only skeletal muscle, brain, and skin located contralaterally to subcutaneously implanted SMT-F tumors had peak [14C]-activities lower than tumor tissue; skin overlying SMT-F tumors showed concentrations not significantly different (P greater than 0.3) from tumor. After 75 days all tissues examined retained some fraction of [14C]-activity, ranging from 16% for kidney to 61% for spleen, of the initial peak tissue levels. The primary route of elimination of Photofrin II was through the bile-gut pathway, with greater than 59% of the administered [14C]-activity recovered in the feces, and only about 6% in the urine, over 192 h. HPLC analyses of fecal extracts showed that mostly monomeric and other low molecular weight porphyrin components of Photofrin II were eliminated. The higher molecular weight oligomeric fractions of Photofrin II were retained in liver and spleen up to 14 days after injection.     

Multilabeled pyrene-functionalized 2'-amino-LNA probes for nucleic acid detection in homogeneous fluorescence assays

Homogeneous fluorescence assays for detection of nucleic acids are widely used in biological sciences. Typically, probes such as molecular beacons that rely on distance-dependent fluorescence quenching are used for such assays. Less attention has been devoted to tethering a single kind of fluorophores to oligonucleotides and exploiting hybridization-induced modulation of fluorescence intensity for nucleic acid detection. Herein, thermal denaturation experiments and fluorescence properties of oligodeoxyribonucleotides containing one or more 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA monomer(s) X are described. These pyrene-functionalized 2'-amino-LNAs display large increases in thermal stability against DNA/RNA complements with excellent Watson-Crick mismatch discrimination. Upon duplex formation of appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA probes and complementary DNA/RNA, intensive fluorescence emission with quantum yields between 0.28 and 0.99 are observed. Quantum yields of such magnitudes are unprecedented among pyrene-labeled oligonucleotides. Molecular modeling studies suggest that the dioxabicyclo[2.2.1]heptane skeleton and amide linkage of monomer X fix the orientation of the pyrene moiety in the minor groove of a nucleic acid duplex. Interactions between pyrene and nucleobases, which typically lead to quenching of fluorescence, are thereby reduced. Duplexes between multiple modified probes and DNA/RNA complements exhibit additive increases in fluorescence intensity, while the fluorescence of single stranded probes becomes increasingly quenched. Up to 69-fold increase in fluorescence intensity (measured at lambda(em) = 383 nm) is observed upon hybridization to DNA/RNA. The emission from duplexes of multiple modified probes and DNA/RNA at concentrations down to less than 500 nM can easily be seen by the naked eye using standard illumination intensities.     

Enhancing glycan stability via site-selective fluorination: modulating substrate orientation by molecular design

Single site OH → F substitution at the termini of maltotetraose leads to significantly improved hydrolytic stability towards α-amylase and α-glucosidase relative to the natural compound. To explore the effect of molecular editing, selectively modified oligosaccharides were prepared via a convergent α-selective strategy. Incubation experiments in purified α-amylase and α-glucosidase, and in human and murine blood serum, provide insight into the influence of fluorine on the hydrolytic stability of these clinically important scaffolds. Enhancements of ca. 1 order of magnitude result from these subtle single point mutations. Modification at the monosaccharide furthest from the probable enzymatic cleavage termini leads to the greatest improvement in stability. In the case of α-amylase, docking studies revealed that retentive C2-fluorination at the reducing end inverts the orientation in which the substrate is bound. A co-crystal structure of human α-amylase revealed maltose units bound at the active-site. In view of the evolving popularity of C(sp³)–F bioisosteres in medicinal chemistry, and the importance of maltodextrins in bacterial imaging, this discovery begins to reconcile the information-rich nature of carbohydrates with their intrinsic hydrolytic vulnerabilities.

Single site OH → F substitution at the termini of maltotetraose leads to significantly improved hydrolytic stability towards α-amylase and α-glucosidase relative to the natural compound.     

2'-Spiro ribo- and arabinonucleosides: synthesis, molecular modelling and incorporation into oligodeoxynucleotides

We have synthesized four conformationally restricted bicyclic 2'-spiro nucleosides via 2'-C-allyl nucleosides as key intermediates. The ribo-configured 2'-spironucleosides 9b and 14b were obtained by a convergent strategy starting from 2-ketofuranose 1 whereas the arabino-configured 2'-spironucleosides 21 and 27 were obtained by a linear strategy with a 2'-ketouridine derivative as starting material. The furanose ring of 9b/14b adopts N-type conformations whereas the furanose ring of 21/27 exists as an N<==>S equilibrium. These compounds showed no anti-HIV-1 activity or cytotoxicity. Incorporation of the four 2'-spironucleosides (as monomers X4 and X5) into oligodeoxynucleotides was accomplished using the phosphoramidite approach on an automated DNA synthesizer. Irrespective of monomeric configuration, hybridization studies revealed that these 2'-spironucleotide monomers (X4 and X5) induce decreased duplex thermostabilities compared with the corresponding DNA:DNA and DNA:RNA duplexes. Molecular modelling indicated that steric constraints are a possible reason for the lowered binding affinities of the modified oligodeoxynucleotides towards complementary single-stranded DNA and single-stranded RNA complements.     

New scaling algorithms for the assignment and minimum mean cycle problems

In this paper we suggest new scaling algorithms for the assignment and minimum mean cycle problems. Our assignment algorithm is based on applying scaling to a hybrid version of the recentauction algorithm of Bertsekas and the successive shortest path algorithm. The algorithm proceeds by relaxing the optimality conditions, and the amount of relaxation is successively reduced to zero. On a network with 2n nodes,m arcs, and integer arc costs bounded byC, the algorithm runs in O( m log(nC)) time and uses very simple data structures. This time bound is comparable to the time taken by Gabow and Tarjan's scaling algorithm, and is better than all other time bounds under thesimilarity assumption, i.e.,C = O(n ^k ) for somek. We next consider the minimum mean cycle problem. Themean cost of a cycle is defined as the cost of the cycle divided by the number of arcs it contains. Theminimum mean cycle problem is to identify a cycle whose mean cost is minimum. We show that by using ideas of the assignment algorithm in an approximate binary search procedure, the minimum mean cycle problem can also be solved in O( m lognC) time. Under the similarity assumption, this is the best available time bound to solve the minimum mean cycle problem.