A primer on perfect simulation for spatial point processes

This primer provides a self-contained exposition of the case where spatial birth-and-death processes are used for perfect simulation of locally stable point processes. Particularly, a simple dominating coupling from the past (CFTP) algorithm and the CFTP algorithms introduced in [13], [14], and [5] are studied. Some empirical results for the algorithms are discussed. Received: 30 June 2002     

3',4'-trans-linked bicyclic nucleosides locked in S-type conformations

A novel class of 3',4'-trans-linked bicyclic nucleosides with locked S-type furanose conformations is introduced by synthesis of two model derivatives; one was obtained by cyclic ether formation and the other by ring-closing metathesis methodology.     

The roles of template complexation and ligand binding conditions on recognition in bupivacaine molecularly imprinted polymers

A model for the molecular basis for ligand recognition in bupivacaine imprinted methacrylic acid-ethylene glycol dimethacrylate co-polymers has been developed based upon a series of (1)H-NMR studies in conjunction with HPLC and radioligand binding analyses. (1)H-NMR studies indicated that functional monomer-template complexes survive the polymerisation process, at least up until the stage of gelation. Polymers were synthesised and characterised by surface area analysis (BET), FT-IR and SEM. A combination of zonal and frontal chromatographic studies in aqueous and non-polar media indicate that selectivity arises from a combination of hydrophobic and electrostatic interactions. However, in the concentration regime employed for LC-based studies, ligand recognition in aqueous media was shown to be predominantly non-specific and hydrophobic in character. Radioligand binding studies, in lower ligand binding concentration regimes, permitted closer examination of the higher affinity binding sites. It was shown that the presence of a polar modifier in a non-polar solvent, or an organic modifier in water, produced enhanced selectivity. Variable temperature studies showed that the temperature of binding influences selectivity as well as the apparent number of sites available and that this effect is different in organic and aqueous environments. This indicates that the system studied is more complex in character than is generally appreciated. A comparison of the techniques employed here indicates that although chromatographic studies provide a valuable first-round screen for polymer-ligand selectivities, the level of detail obtainable using radioligand binding studies (lower concentrations and true equilibrium binding) makes them superior for detailed evaluations of molecularly imprinted polymers.     

N-methylpiperazinocarbonyl-2',3'-BcNA and 4'-C-(N-methylpiperazino)methyl-DNA: introduction of basic functionalities facing the major groove and the minor groove of a DNA:DNA duplex

Piperazino-functionalized 2',3'-BcNA and 4'-C-hydroxymethyl-DNA are appropriate molecular architectures for the introduction of basic functionalities facing the major groove and the minor groove of nucleic acid duplexes, respectively. 4'-C-(N-Methylpiperazino)methyl-DNA monomers induce significantly increased thermal stability of a DNA:DNA duplex.     

Oligodeoxynucleotide analogues containing 3′-deoxy-3′-C-threo-hydroxymethylthymidine: Synthesis, hybridization properties and enzymatic stability

Novel Oligodeoxynucleotide analogues containing 3′-C-threo-methylene phosphodiester internucleoside linkages were synthesized on automated DNA-synthesizers using the phosphoramidite approach. The sugar modified phosphoramidite building block 5 was obtained by phosphitylation of 1-(2,3-dideoxy-5-O-(4,4′-dimethoxytrityl)-3-C-hydroxymethyl-β-D-threo-pentofuranosyl)thymine (4) which was synthesized in only three steps from 5′-O-(4,4′-dimethoxytrityl)thymidine (1). The hybridization properties and enzymatic stability of the oligonucleotide analogues were studied by UV experiments. 17-Mers having one or three modifications in the middle or two modifications in each end hybridized to DNA with moderate lowered affinity compared to unmodified 17-mers (ΔT_m 1–3°C per modification). Furthermore, the end-modified and all-modified oligonucleotides were stable towards snake venom phosphodiesterase.     

Mimicking the two-dimensional spectrochemical series using density functional computations

With tetragonal distortions of tetrahedral d2 complexes as examples, nonadditive and additive ligand fields are compared computationally, using Kohn-Sham density functional theory (KS-DFT) and ligand-field theory to obtain 45 linear, parametrical equations. For each complex, a "data" reduction from three nonadditive-field parameters to two parameters of the additive field occurs. The complexes V and CrX4- (where X=F, Cl, Br, I) provide the two-dimensional spectrochemical series of the sigma and pi AOM parameters, which are known semiempirically for the halide ligands. The same parametrical results can be obtained from the Kohn-Sham orbital energies of the "average of configuration" computation.     

Ruthenium Complexes Containing "Noninnocent" o-Benzoquinone Diimine/o-Phenylenediamide(2-) Ligands. Synthesis and Crystal Structure of the Nitrido-Bridged Complex [{LRu(o-C(6)H(4)(NH)(2))}(2)(&mgr;-N)](PF(6))(2).3CH(3)CN.C(6)H(5)CH(3)

Reaction of LRu(III)Cl(3) (L = 1,4,7-trimethyl-1,4,7-triazacyclononane) with 1,2-phenylenediamine (opdaH(2)) in H(2)O in the presence of air affords [LRu(II)(bqdi)(OH(2))](PF(6)) (1), where (bqdi) represents the neutral ligand o-benzoquinone diimine. From an alkaline methanol/water mixture of 1 was obtained the dinuclear species [{LRu(II)(bqdi)}(2)(&mgr;-H(3)O(2))](PF(6))(3) (1a). The coordinated water molecule in 1 is labile and can be readily substituted under appropriate reaction conditions by acetonitrile, yielding [LRu(II)(bqdi)(CH(3)CN)](PF(6))(2) (2), and by iodide and azide anions, affording [LRu(II)(bqdi)I](PF(6)).0.5H(2)O (3) and [LRu(bqdi)(N(3))](PF(6)).H(2)O (4), respectively. Heating of solid 4 in vacuum at 160 degrees C generates N(2) and the dinuclear, nitrido-bridged complex [{LRu(o-C(6)H(4)(NH)(2))}(2)(&mgr;-N)](PF(6))(2) (5). Complex 5 is a mixed-valent, paramagnetic species containing one unpaired electron per dinuclear unit whereas complexes 1-4 are diamagnetic. The crystal structures of 1, 1a.3CH(3)CN, 3, 4.H(2)O, and 5.3CH(3)CN.0.5(toluene) have been determined by X-ray crystallography: 1 crystallizes in the monoclinic space group P2(1)/m, Z = 2, with a = 8.412(2) ?, b = 15.562(3) ?, c = 10.025 ?, and beta = 109.89(2) degrees; 1a.3CH(3)CN, in the monoclinic space group C2/c, Z = 4, with a = 19.858(3) ?, b = 15.483(2) ?, c = 18.192(3) ?, and beta = 95.95(2) degrees; 3, in the orthorhombic space group Pnma, Z = 4, with a = 18.399(4) ?, b = 9.287(2) ?, and c = 12.052(2) ?, 4.H(2)O, in the monoclinic space group P2(1)/c, Z = 4, with a = 8.586(1) ?, b = 15.617(3) ?, c = 16.388(5) ?, and beta = 90.84(2) degrees; and 5.3CH(3)CN.0.5(toluene), in the monoclinic space group P2(1)/c, Z = 4, with a = 15.003(3) ?, b = 16.253(3) ?, c = 21.196(4) ?, and beta = 96.78(3) degrees. The structural data indicate that in complexes 1-4 the neutral o-benzoquinone diimine ligand prevails. In contrast, in 5 this ligand has predominantly o-phenylenediamide character, which would render 5 formally a mixed-valent Ru(IV)Ru(V) species. On the other hand, the Ru-N bond lengths of the Ru-N-Ru moiety at 1.805(5) and 1.767(5) ? are significantly longer than those in other crystallographically characterized Ru(IV)=N=Ru(IV) units (1.72-1.74 ?). It appears that the C(6)H(4)(NH)(2) ligand in 5 is noninnocent and that formal oxidation state assignments to the ligands or metal centers are not possible.     

An average-of-configuration method for using Kohn-Sham density functional theory in modeling ligand-field theory

The Amsterdam Density Functional (ADF) package has been used to constrain Kohn-Sham DFT in such a fashion that a transition from KS-DFT to ligand-field theory in the form of the parametrical d(q)() model is completely well-defined. A relationship is established between the strong-field approximation of the parametrical d(2) model for the tetrahedral complexes VCl(4)(-) and VBr(4)(-) and certain fixed-orbital ADF-computed energies. In this way values for all the parameters of the d(2)() model may be computed, thus allowing the ADF results to be expressed in terms of a KS-DFT energy matrix that can be diagonalized. This means that the KS-DFT deficiency with regard to computation of nondiagonal elements has been overcome and the KS-DFT eigenenergies have become available through the KS-DFT mimicking of the ligand-field plus repulsion model. By using mutually orthogonal strong-field energy matrices, the mimicking has been further elucidated. The computed values for the empirical parameters of VCl(4)(-) and VBr(4)(-) are in good agreement with experimental data. The spectrochemical and the nephelauxetic series have been computed by including the remaining halide complexes and the quantitatively special position of F(-)() among the halides corroborated for both series.