R. de Gelder

Direct determination of molecular constants from rovibronic spectra with genetic algorithms

It is shown that a new procedure, based on genetic algorithms (GA’s), can be used for direct determination of molecular constants, in particular rotational constants, from rovibronic spectra. This new approach only requires an estimate of the acceptable range of the parameters. The power of the method is demonstrated on the rotationally resolved fluorescence spectra of indole, indazole, benzimidazole, and 4-aminobenzonitril. A rigid asymmetric rotor Hamiltonian is used to calculate the theoretical spectra. The GA matches the generated spectra with an experimental spectrum with the use of a new method for spectra comparison. This spectra comparison function is able to deal with frequency shifts which are caused by (small) changes in the rotational constants and it yields better results in comparison with traditional spectra comparison methods, like RMS. In addition, the robustness of the method is tested.

A generalized expression for the similarity of spectra: application to powder diffraction pattern classification

A generalized expression is given for the similarity of spectra, based on the normalized integral of a weighted crosscorrelation function. It is shown that various similarity and dissimilarity criteria previously described in literature can be written as special cases of this general expression. A new similarity criterion, based on this generalized expression, is introduced. The benefits of this criterion are that it properly recognizes shifted but otherwise similar details in spectra and that the resulting similarity measure is normalized. Moreover, the criterion can easily be adapted to specific properties of spectra resulting from various analytical methods. The new criterion is applied to the classification of a series of crystal structures of cephalosporin complexes, based on comparison of their calculated powder diffraction patterns. The results are compared with those obtained using previously described criteria.

Organocatalytic Enantioselective Total Synthesis of (−)-Arboricine

The tetracyclic indole alkaloid (-)-arboricine has been prepared using an asymmetric organocatalytic Pictet-Spengler reaction as the key step followed by a diastereoselective Pd-catalyzed iodoalkene/enolate cyclization. The absolute stereochemistry was unequivocally proven by X-ray crystallographic analysis and appeared to be opposite to the published structure in the original paper.

Tomato-produced 7-epizingiberene and R-curcumene act as repellents to whiteflies

How whiteflies (Bemisia tabaci) make the choice for a host plant prior to landing, is not precisely known. Here we investigated whether they respond to specific volatiles of tomato. Zingiberene and curcumene were purified from Solanum habrochaites (PI127826), characterised by NMR and X-ray analysis and identified as 7-epizingiberene and R-curcumene. In contrast, oil from Zingiber officinalis contained the stereoisomers zingiberene and S-curcumene, respectively. Using a combination of free-choice bio-assays and electroantennography, 7-epizingiberene and its dehydrogenated derivative R-curcumene were shown to be active as semiochemicals to B. tabaci adults, whereas the stereoisomers from ginger were not. In addition, R-curcumene elicited the strongest electroantennographic response. Bio-assays showed that a cultivated tomato could be made less attractive to B. tabaci than its neighbouring siblings by the addition of the tomato stereoisomer 7-epizingiberene or its derivative R-curcumene. These sesquiterpenes apparently repel adult whiteflies prior to landing, presumably because it informs them that after landing they, or their offspring, may be exposed to higher and lethal concentrations of the same compounds.

Automatic determination of crystal structures using Karle–Hauptman matrices

This paper describes a method for automatic structure determination by the application of Karle–Hauptman matrices to the phase problem. A new method, the common-minor strategy, is used to combine the information contained in several Karle–Hauptman matrices. Sets of phases large enough to define the structure are obtained. If the matrices are linked properly, phases contained in a larger array of matrices can be adequately restricted to a common origin. The partial solutions obtained on Fourier transformation are extended to the complete structure in a fully automatic manner. A new algorithm is presented for the maximization of the determinant of a Karle–Hauptman matrix as a function of the phases.

Clathrate-Type Complexation of Cephalosporins withβ-Naphthol

The cephalosporin antibiotics cephalexin, cephradine, cefaclor, and cefadroxil form clathrate-type complexes with β-naphthol in the solid state (depicted here). The crystal structures and packing forces are unraveled.

Crystal structure of the ordered perovskite: BaBi0.5Sb0.5O3

The structure of BaBi{sub 0.5}Sb{sub 0.5}O{sub 3} is determined by single crystal X-ray diffraction. It is an ordered perovskite, having rhombohedral symmetry, space group R {bar 3}m (No. 166), with lattice parameters a = 6.043(1) {angstrom} and {alpha} = 60.05(2)(degree). The final agreement factor R based on F{sup 2} for 6420 reflections was 0.052. An important structural feature of BaBi{sub 0.5}Sb{sub 0.5}O{sub 3} is the displacements of oxygen atoms from their ideal positions within the pseudo-cubic [110]{sub p} planes, creating an alternative arrangement of (larger) BiO{sub 6} and (smaller) SbO{sub 6} octahedra. Therefore, the valence states of bismuth and antimony can be readily assigned as Bi(III) and Sb(V).

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.

Powder pattern indexing using the weighted crosscorrelation and genetic algorithms.

X‐ray diffraction is a powerful technique for investigating the structure of crystals and crystalline powders. Unfortunately, for powders, the first step in the structure elucidation process, retrieving the unit cell parameters (indexing), is still very critical. In the present article, an improved approach to powder pattern indexing is presented. The proposed method matches peak positions from experimental X‐ray powder patterns with peak positions from trial cells using a recently published method for pattern comparison (weighted crosscorrelation). Trial cells are optimized with Genetic Algorithms. Patterns are not pretreated to remove any existing zero point shift, as this is determined during optimization. Another improvement is the peak assignment procedure. This assignment is needed for determining the similarity between lines from trial cells and experiment. It no longer allows calculated peaks to be assigned twice to different experimental peaks, which is beneficial for the indexing process. The procedure proves to be robust with respect to false peaks and accidental or systematic absensences of reflections, and is successfully applied to powder patterns originating from orthorhombic, monoclinic, and triclinic compounds measured with synchrotron as well as with conventional laboratory X‐ray diffractometers.

The hydration/dehydration behavior of aspartame revisited.

Aspartame, l-aspartyl-l-phenylalanine methyl ester, has two hydrates (IA and IB), a hemi-hydrate (IIA) and an anhydrate (IIB). The hydration/dehydration behavior of aspartame was investigated using hot-humidity stage X-ray powder diffraction (XRPD) and molecular mechanics modeling in combination with differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). The results of this study are compared to earlier studies on aspartame as described in literature. It is shown that earlier transition studies were hampered by incomplete conversions and wrong assignment of the forms. The combination of the techniques applied in this study now shows consistent results for aspartame and yields a clear conversion scheme for the hydration/dehydration behavior of the four forms.