Thirty years of pyrimidine chemistry in the laboratory of organic chemistry at the Wageningen Agricultural University,The Netherlands (review)

In this review attention is paid to two topics, which were of great interest to us during 30 years of studies in pyrimidine chemistry in our laboratory: first, the development of our concepts of the AIYRORC processes, which occur in ring transformation reactions; second, the intra- and intermolecular inverse Diels-Alder reactions in which the pyrimidine ring acts as the electron poor diazadiene system. Their use in synthetic chemistry is illustrated and evidence is presented, based on experiments and molecular mechanics calculations, that in intermolecular Diels-Alder reactions the geometry of the side-chain plays a vital role.     

α-Diimines as monodentate or bridging ligands; synthesis and characterization of palladium(II) and rhodium(I) di(t-butyl)diimine complexes

Complexes of di(t-butyl)diimine with PdCl₂(PhCN)₂ and with (CO)₂RhCl dimer have been synthesized and characterized. The diimine ligand is monodentate bonded in PdCl₂(t-butyldiimine)₂, while in (t-butyldiimine)-[Rh(CO)₂Cl]₂ it bridges two Cl(CO)₂Rh units.     

Regioselectivity in SNH reactions of some 3-nitro-1,8-naphthyridines with chloromethyl phenyl sulfone

A number of 2-X-3-nitro-1,8-naphthyridines (X= H,D,OH,Cl,NH₂, OEt) react with the anion of chloromethyl phenyl sulfone exclusively into 2-X-3-nitro-4-(phenylsulfonylmethyl)-1,8-naphthyridines in high yield. The reaction is found by quantum chemical calculations to be controlled by the interactions of the HOMO of the nucleophile with the LUMO of the substrate, and not by charge.     

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

PHOTOREAaIVITY OF CHLORAMPHENICOL in vitro AND in vivo

Abstract The negative side effects of chlorarnphenicol (CAP) mostly involve blood dyscrasias (e.g. irreversible nondose-dependent aplastic anemia), allergic skin reactions and eye damage. To learn the cause of these side effects, most research focuses on metabolically formed nitroso- and hydroxylamino derivatives in the predisposed patient. In previous investigations it was demonstrated that photochemical decomposition of CAP in vitro by UV-A leads to formation of p-nitrobenzaldehyde (pNB), p-nitrobenzoic acid (pNBA) and p-nitrosobenzoic acid (pNOBA); the latter comprises up to 45 mol% of the starting amount of CAP. Incubation of these photoproducts in rat blood showed that pNB and pNOBA rapidly react and that PNBA is stable under these conditions. Reaction products from pNB (half-life 1.7 min) proved to be pNBA and p-nitrobenzyl alcohol (pNBOH) while pNOBA (half-life 3.7 min) was converted into p-aminobenzoic acid (pABA). Exposure of CAP in rat blood to UV-A yielded the same end products: pNBA, PABA and pNBOH. To estimate the amount of oxidative stress generated in vivo by these compounds, the ability to form methemoglobin (MetHb) in erythrocytes was tested; only pNOBA and p-hydroxylaminobenzoic acid (pHABA), a possible intermediate in the decomposition of pNOBA, proved to be reactive. Ultraviolet-A exposure of rats, after intraperitoneal injection of CAP, led to 3.6 times the basic level of MetHb. In addition, covalent binding of ³H-labeled CAP photoproducts to the skin of the back and to the ears was found, which was 9.1 and 3.2 times higher, respectively, than the dark values. Toxicity toward bone marrow cells of all photoproducts was established in vitro. p-Nitrobenzaldehyde, pNOBA andpHABA were 20, 6 and 6 times more toxic than CAP, respectively. These results show that photodecomposition of CAP in vivo does occur. Its reactive photoproducts are able to cause damage that may lead to (systemic) side effects. The latter is supported by the fact that the nature of the reactive products, nitroso- and hydroxylamino derivatives, is the same as the expected metabolites.     

Effects of Ultraviolet-B Exposure on the Resistance to Listeria monocytogenes in the Rat

A rat infection model using the bacterial pathogen Listeria monocytogenes was employed to analyze the im-munosuppressive activity of UVB radiation. Rats were exposed to suberythemal doses of UVB radiation for 5 or 7 consecutive days, using Kromayer or FS40 lamps respectively. Subsequently, the rats were infected subcuta-neously or intravenously with Listeria . Exposure to UVB resulted in an increased number of bacteria in the spleen 4 days after infection. Listeria -specific lymphocyte proliferation assays as well as delayed-type hypersensitivity reactions demonstrated that T cell-mediated immunity to Listeria was impaired by UVB as measured 4 and 8 days after infection. In addition, UVB exposure decreased phagocytotic activity of peripheral blood macrophages. This study demonstrated that suberythemal doses of UVB radiation caused a delay in the clearance of Listeria bacteria from the spleen of the rats and that this was probably caused by impaired nonspecific phagocytosis of Listeria by macrophages in addition to an impaired activity of Listeria -specific T cells.     

Commutative and noncommutative representations of matrix-valued herglotz-nevanlinna functions

Operator realizations of matrix-valued Herglotz-Nevanlinna functions play an important and essential role in system theory, in the spectral theory of bounded nonselfadjoint operators, and in interpolation problems. Here, a generalization for realization results of the Brodskiǐ-Livsic type is given for Herglotz-Nevanlinna functions whose spectral measures are compactly supported.     

Quasi-periodic stability of normally resonant tori

We study quasi-periodic tori under a normal-internal resonance, possibly with multiple eigenvalues. Two non-degeneracy conditions play a role. The first of these generalizes invertibility of the Floquet matrix and prevents drift of the lower dimensional torus. The second condition involves a Kolmogorov-like variation of the internal frequencies and simultaneously versality of the Floquet matrix unfolding. We focus on the reversible setting, but our results carry over to the Hamiltonian and dissipative contexts.     

SYNTHESIS AND CONFORMATIONAL STUDIES OF A NUMBER OF SATURATED BICYCLIC SIX-MEMBERED RING PHOSPHITES

Abstract

An ¹H NMR study of the conformation of the dioxaphosphorinane ring of a number of diastereoisomeric bicyclic saturated six-membered ring phosphites (3ab-10ab) has been performed. The dioxaphosphorinane ring of these phosphites is transannelated with a tetrahydrofuran, cyclopen-tane, tetrahydropyran or cyclohexane ring. The substituent on the phosphorus atom is a methoxy or phenoxy group. It is shown that the cis isomers 3a-10a prefer a chair conformation of the dioxaphosphorinane ring, independent of the substituent on the phosphorus atom and of the nature of the transannelated ring. In contrast, for the trans isomers 3b-10b a twist rather than a chair conformation of the dioxaphosphorinane ring is preferred. The fraction of the twist conformer in the trans isomers is mainly determined by the substituent on phosphorus. The size and composition of the transannelated ring are relatively unimportant in this respect. For both cis and trans isomers the preferred geometry is solvent-independent. The measured ^3JPOCH couplings of the cis isomers 3a-10a are used to formulate an expression for the dependence of such couplings upon dihedral angles in bicyclic phosphites.     

EC–SPE–stripline-NMR analysis of reactive products: a feasibility study

Flow-through electrochemical conversion (EC) of drug-like molecules was hyphenated to miniaturized nuclear magnetic resonance spectroscopy (NMR) via on-line solid-phase extraction (SPE). After EC of the prominent p38α mitogen-activated protein kinase inhibitor BIRB796 into its reactive products, the SPE step provided preconcentration of the EC products and solvent exchange for NMR analysis. The acquisition of NMR spectra of the mass-limited samples was achieved in a stripline probe with a detection volume of 150 nL offering superior mass sensitivity. This hyphenated EC–SPE–stripline-NMR setup enabled the detection of the reactive products using only minute amounts of substrate. Furthermore, the integration of conversion and detection into one flow setup counteracts incorrect assessments caused by the degradation of reactive products. However, apparent interferences of the NMR magnetic field with the EC, leading to a low product yield, so far demanded relatively long signal averaging. A critical assessment of what is and what is not (yet) possible with this approach is presented, for example in terms of structure elucidation and the estimation of concentrations. Additionally, promising routes for further improvement of EC–SPE–stripline-NMR are discussed.