František Pavelčík

Synthesis and characterization of a new heteroligand vanadium(v) oxo-monoperoxo complex and first crystal structure with coordinated N-(carbamoylmethyl)iminodiacetate

Abstract Formation of a vanadium(V) monoperoxo complex with coordinated N-(carbamoylmethyl)iminodiacetate2− (ada) was observed in the pH range 1.3–8.6. The MI[VO(O2)ada] · xH2O (MI= K+, Cs+; x = 4 for K+ and 1 for Cs+) and Ba[VO(O2) ada]2 · 3H2O complexes were isolated from aqueous solution. K[VO(O)2)ada]·H2O was obtained by thermal decomposition of the crystallohydrate. The crystal structure of K[VO(O2)ada] · 4H2O was determined by X-ray structure analysis. The vanadium atom is seven-coordinated by oxo, η2-peroxo and tetradentate ada2−-N,O1, O2, O3 ligands. The oxygen of the carbamoyl group is in the apical position trans to the VO group.

The first tetranuclear vanadium(V) peroxo complex: Preparation, vibrational spectra and X-ray crystal structure of K6[V4O4(O2)8(PO4)]·9H2O

Abstract The vanadium(V) peroxo phosphato complex K 7 [V 4 O 4 (O 2 ) 8 (PO 4 )]·9H 2 O has been obtained from the KVO 3 KH 2 PO 4 KOHH 2 O 2 H 2 OC 2 H 5 OH system. The X-ray structural analysis revealed a tetranuclear anionic structure in which two dinuclear [V 2 O 2 (O) 2 ) 2 ( μ - η 1 : η 2 -O 2 ) 2 ] units are connected by the μ 4 -PO 4 group.

Simple procedure for conformation-family search in multidimensional torsion-angle space

A method for studying conformation spaces in n dimensions has been developed. The method is used to calculate preferences of conformation families for the purpose of model building.

Synthesis, characterization, and crystal and molecular structures of caesium N-(carbamoylethyl)iminodiacetatooxoperoxovanadate(V) monohydrate

A new monoperoxo complex of vanadium(V) of composition Cs[VO(O2)(CEIDA)]·H2O [where H2CEIDA is N-(carbamoylethyl)iminodiacetic acid] was prepared and characterized by IR, UV-VIS and 51V NMR spectroscopies. Thermal analysis showed that after crystal water release the anhydrous Cs[VO(O2)(CEIDA)] is formed, which is stable over a relatively large temperature interval and can be isolated by interruption of the dynamic heating in that interval. The X-ray structure analysis of Cs[VO(O2)(CEIDA)]·H2O revealed a mononuclear structure of the complex anion with a typical distorted pentagonal bipyramidal arrangement around vanadium formed by two peroxo oxygens bound in an η2-fashion, two oxygens from the deprotonated carboxylic groups and a nitrogen in the equatorial plane, and an oxo ligand and an oxygen from the carbamoyl group in the apical positions. The heteroligand is thus bound as a tetradentate CEIDA(2-)-N,O,O,O ligand to form one six-membered and two glycinate rings.

Phased rotation, conformation and translation function: theory and computer program

A new crystallographic function, phased rotation conformation and translation (PRCTF), has been developed. The function is designed for automatic interpretation of electron density utilizing molecular fragments with some conformational freedom. A computer program, NUT, has been written for the calculation of the PRCTF.

Patterson-oriented automatic structure determination. Organic structures

Automatic Patterson methods combined with Fourier recycling have been applied to the determination of organic structures. Test calculations showed that these methods can be useful alternatives to traditional direct methods.

HEL – a program for model building based on a phased rotation, conformation and translation function

HEL is a program for creating continuous chains of polypeptides or polynucleotides from positioned fragments. Structure fragments are located by the program NUT, which performs a phased rotation, conformation and translation function. The output of HEL is a PDB file.

Crystal and molecular structure of Δ-cis-α-ethylenebis-S-prolinato(1,2-diamino-ethane)cobalt(III) perchlorate dihydrate, Δ-cis-α-[Co(ss-EBP)(en)] ClO4·2H2O

Abstract The crystal and molecular structure of Δ- cis -α- ethylenebis-S-prolinato(1,2-diaminoethane)cobalt(III) perchlorate dihydrate, Δ- cis -α-[Co(SS-EBP)(en)] ClO 4 · 2H 2 O, was determined from three-dimensional X-ray diffractometer data. The complex crystallizes in the orthorhombic system, space group P 2 1 2 1 2 1 with a = 7.879(4) A, b = 13.738(9) A, c = 19.445(2) A, V = 2104(2) A 3 . With Z = 4, the observed and calculated densities are 1.60(2) and 1.605 g cm −3 , respectively. The structure was refined by the block- diagonal least-squares technique to a final R = 0.0560 for 1604 observed reflections. The geometry about the cobalt atom is roughly octahedral with the tetradentate SS-EBP (= ethylenebis-S-prolinate ion), assuming cis -α configuration in which the complex possesses two out-of-plane amino acidate (R) rings and the backbone ethylenediamine (E) ring. The E ring conformation is δ. On the other hand, the R rings have λ conformation as well as the en ring. Δ-R N R N− (δ E  λ R 1  λ R 2 )(λ en )- cis -α-[Co(SS-EBP)(en)] + is one of two possible isomers of this compound which have been isolated and whose absolute configurations have been tentatively assigned by spectroscopy. The crystal and molecular structure determination confirms these assignments.

Patterson oriented automatic structure determination: superposition pseudosymmetry

An automatic structure determination method based on an interpretation of the Patterson function has been improved by utilizing information on superposition pseudosymmetry. This pseudosymmetry can be detected using MIF (multiple implication function) groups. A new method of structure determination based on an enantioselective cross-vector function and on a sum atomic minimum superposition is introduced. This new method seems to be suitable for equal-atom structures. The reliability and speed of the structure determination has been increased.

Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a constrained real-space refinement of molecular fragments and a phased rotation–conformation–translation function. Real-space refinement has also contributed to the improvement of the bone/base method of RNA model building and to redesigning the method of building double helices in nucleic acid structures. This improvement is reflected in the increased accuracy of the model building and the ability to better distinguish between correct and false solutions. A program, RSR, was created, and the programs NUT, HEL and DHL were upgraded and organized into a program system, which is CCP4 oriented. Source codes will also be released.