Biomedical subjects

R de Gelder

Publications and source records attributed to R de Gelder.

8 recordsLinked to original sources

PubMed2006

"Clickphine": a novel and highly versatile P,N ligand class via click chemistry.

[Structure: see text] A novel P,N-type ligand family (ClickPhine) is disclosed that is easily accessible using the Cu(I)-catalyzed azide-alkyne "click" cycloaddition. A diverse set of ligands was made in just three steps from readily available starting materials to give several homogeneous and a heterogeneous catalyst. Preliminary experiments show the efficacy of these ligands in the Pd-catalyzed allylic alkylation reaction.

Journal Article↗

PubMed2005

Remarkable features in lattice-parameter ratios of crystals. I. Orthorhombic, tetragonal and hexagonal crystals.

The investigation of the lattice-parameter ratios of tetrahedral and hexagonal-rhombohedral inorganic compounds, as reported by Constant & Shlichta [(2003), Acta Cryst. A59, 281-282], has been extended to the structural data found for organic and metal-organic compounds (CSD), for bio-macromolecular crystals (PDB) and for inorganic materials (ICSD). In this first part of the series, the frequency distribution of orthorhombic, tetragonal and hexagonal crystals is presented. The results obtained confirm the existence of sharp peaks as a function of the ratios of lattice parameters and reveal additional exponential components, decaying for large and small values of these ratios. Practically all the important peaks occur at ratios which correspond to lattices having metric tensors with rational entries, the so-called integral lattices. The exponential component is interpreted as expressing a general statistical distribution which is valid for the generic crystal lattices, i.e. those normally considered. The exponential fraction dominates the peaked component in the organic and metal-organic cases, is less important for bio-macromolecular crystals and is much less important than the sharp peaks for inorganic crystals. Remarkable is the crystallographic relevance of the isometric hexagonal lattice, characterized by the axial ratio c/a = 1 and first observed in the molecular form of a protein. In the frequency distribution of 12 117 inorganic hexagonal crystals, the highest peak of 937 crystals occurs for c = a. In the hexagonal case of the bio-macromolecules the most important peak of 422 crystals is observed near the ideal h.c.p. (hexagonal closed packing) ratio of (8/3)(1/2).

Crystallization↗

PubMed2005

Remarkable features in lattice-parameter ratios of crystals. II. Monoclinic and triclinic crystals.

The frequency distributions of monoclinic crystals as a function of the lattice-parameter ratios resemble the corresponding ones of orthorhombic crystals: an exponential component, with more or less pronounced sharp peaks, with in general the most important peak at the ratio value 1. In addition, the distribution as a function of the monoclinic angle beta has a sharp peak at 90 degrees and decreases sensibly at larger angles. Similar behavior is observed for the three triclinic angular parameters alpha, beta and gamma, with characteristic differences between the organic and metal-organic, bio-macromolecular and inorganic crystals, respectively. The general behavior observed for the hexagonal, tetragonal, orthorhombic, monoclinic and triclinic crystals {in the first part of this series [de Gelder & Janner (2005). Acta Cryst. B61, 287-295] and in the present case} is summarized and commented. The data involved represent 366 800 crystals, with lattice parameters taken from the Cambridge Structural Database, CSD (294 400 entries), the Protein Data Bank, PDB (18 800 entries), and the Inorganic Crystal Structure Database, ICSD (53 600 entries). A new general structural principle is suggested.

Crystallization↗

PubMed2005

Method for the computational comparison of crystal structures.

A new method for assessing the similarity of crystal structures is described. A similarity measure is important in classification and clustering problems in which the crystal structures are the source of information. Classification is particularly important for the understanding of properties of crystals, while clustering can be used as a data reduction step in polymorph prediction. The method described uses a radial distribution function that combines atomic coordinates with partial atomic charges. The descriptor is validated using experimental data from a classification study of clathrate structures of cephalosporins and data from a polymorph prediction run. In both cases, excellent results were obtained.

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PubMed2001

beta -Helical polymers from isocyanopeptides.

Polymerization of isocyanopeptides results in the formation of high molecular mass polymers that fold in a proteinlike fashion to give helical strands in which the peptide chains are arranged in beta-sheets. The beta-helical polymers retain their structure in water and unfold in a cooperative process at elevated temperatures. The peptide architecture in these polymers is a different form of the beta-helix motif found in proteins. Unlike their natural counterparts, which contain arrays of large beta-sheets stacked in a helical fashion, the isocyanopeptide polymers have a central helical core that acts as a director for the beta-sheet-like arrangement of the peptide side arms. The helical structure of these isocyanopeptide polymers has the potential to be controlled through tailoring of the side branches and the hydrogen-bonding network present in the beta-sheets.

Alanine↗

PubMed2001

Molecular clips based on propanediurea: exceptionally high binding affinities for resorcinol guests.

A series of new receptor molecules derived from 2,4,6,8-tetraazabicyclo[3.3.1]nonane-3,7-dione (propanediurea) is described. These molecules possess a cavity which is defined by two nearly parallel aromatic side walls positioned on top of a bis-urea framework. The resulting "U-shaped" clip molecules are ideal hosts for the complexation of flat aromatic guest molecules. The affinity of these new propanediurea based molecular clips for dihydroxybenzene derivatives is exceptionally high, with association constants up to K(a) = 2 400 000 L mol(-)(1). Comparison of the binding mechanism of a variety of clip and half clip hosts, in conjunction with NMR, IR, and X-ray studies, has enabled the reason for this high binding to be elucidated. It is shown that subtle sub-angstrom changes in the geometry of the clip molecules have a great impact on their binding properties.

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PubMed2001

Lamellar organic thin films through self-assembly and molecular recognition.

Molecular clips possessing U-shaped cavities have been functionalized on their convex side with long aliphatic tails. These molecules form dimers which self-assemble into malleable lamellar thin films. Upon addition of a guest (methyl 3,5-dihydroxybenzoate), a 1:1 host-guest complex is formed, which prohibits clip dimerization. As a result, the lamellar structure of the material is lost. Complexation of 3,5-dihydroxybenzoic acid in the clip results in host-guest complexes which dimerize by hydrogen bonding interactions between the carboxylic acid functions of the bound guests. This dimerization restores the lamellar type architecture of the material.

Journal Article↗

PubMed2000

2-rhodaoxetanes: their formation of oxidation of [RhI(ethene)]+ and their reactivity upon protonation.

New cationic, pentacoordinate complexes [(TPA)Rh1(ethene)]+, [1a]+, and [(MeTPA)Rh1(ethene)]+, [1b]+, have been prepared (TPA = N,N,N-tri(2-pyridylmethyl)amine, MeTPA = N-[(6-methyl-2-pyridyl)-methyl]-N,N-di(2-pyridylmethyl)amine). Complex [1a]+ is selectively converted by aqueous HCl to [(TPA)RhIII-(ethyl)Cl]+, [2a]+. The same reaction with [1b]+ results in the [(MeTPA)RhIII-(ethyl)Cl]+ isomers [2b]+ and [2c]+. Treatment of [1a]+ and [1b]+ with aqueous H2O2 results in a selective oxygenation to the unsubstituted 2-rho-da(III)oxetanes (1-oxa-2-rhoda(III)cyclo-butanes) [(TPA)RhIII(kappa2-C,O-2-oxyethyl)]+, [3a]+, and [(MeTPA)RhIII(kappa2-C,O-2-oxyethyl)]+, [3b]+. The reactivity of 2-rhodaoxetanes [3a]+ and [3b]+ is dominated by the nucleophilic character of their 2-oxyethyl oxygen. Reaction of [3a]+ and [3b]+ with the non-coordinating acid HBAr(f)4 results in the dicationic protonated 2-rhodaoxetanes [(TPA)RhIII(kappa2-2-hydroxyethyl)]2+, [4a]2+, and [(MeTPA)RhIII(kappa2-2-hydroxyethyl)]2+, [4b]2+. These eliminate acetaldehyde at room temperature, probably via a coordinatively unsaturated kappa1-2-hydroxyethyl complex. In acetonitrile, complex [4a]2+ is stabilised as [(TPA)-RhIII(kappa1-2-hydroxyethyl)(MeCN)]2+, [5a]2+, whereas the MeTPA analogue [4b]2+ continues to eliminate acetaldehyde. Reaction of [3a]+ with NH4Cl and Mel results in the coordinatively saturated complexes [(TPA)RhIII(kappa1-2-hydroxyethyl)(Cl)]+, [6a]+, and [(TPA)-RhIII(kappa1-2-methoxyethyl)(I)+, [7a]+, respectively. Reaction of [3a]+ with NH4+ in MeCN results in formation of the dicationic metallacyclic amide [(TPA)-RhIII [kappa2-O,C-2-(acetylamino)ethyl]]2+, [9]2+, via the intermediates [4a]2+, [5a]2+ and the metallacyclic iminoester [(TPA)RhIII[kappa2-N,C-2-(acetimidoyloxy)ethyl]]2+, [8]2+. The observed overall conversion of the [Rh(I)(ethene)] complex [1a]+ to the metallacyclic amide [9]2+ via 2-rhodaoxetane [3a]+, provides a new route for the amidation of a [RhI(ethene)] fragment.

Journal Article↗