Bernt Krebs

Bio: Bernt Krebs is an academic researcher from University of Münster. The author has contributed to research in topics: Crystal structure & Ligand. The author has an hindex of 56, co-authored 729 publications receiving 16336 citations. Previous affiliations of Bernt Krebs include Leiden University & Clariant.

X-ray absorption spectroscopic studies of zinc in the N-terminal domain of HIV-2 integrase and model compounds.

Abstract: X-ray absorption spectroscopy (XAS), including extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) analysis, has been carried out at the Zn K edge of the N-terminal part of the integrase protein of the human immunodeficiency virus, type 2 (HIV-2), and of some zinc coordination compounds. In the presence of excess beta-mercaptoethanol, which was present in the NMR structure elucidation of the protein [Eijkelenboom et al. (1997), Curr. Biol. 7, 739-746; (2000), J. Biomol. NMR, 18, 119-28], the protein spectrum was nearly identical to that recorded in its absence. Comparison of the XANES of the protein with that of model compounds and literature data permits the conclusion that the Zn ion is four-coordinated. The major shell of the EXAFS provides evidence for a mixed (N or O as well as S) coordination sphere, while the minor shells indicate imidazole coordination. Our approach to the analysis of the EXAFS, including quantification of the imidazole by multiple scattering simulations with EXCURV92, was validated on the model compounds. An important result is that with multiple scattering simulations using restraints on the parameters of the imidazole rings the number of imidazoles and their orientation could be determined. The integrase spectra can be fitted with two sulfur ligands at 2.26 A (Debye-Waller-type factor 0.009 A(2)) and two imidazole ligands with the N atoms at 1.99 A (Debye-Waller-type factor 0.005 A(2)). The XAS-derived geometry is fully consistent with that found in the NMR structure determination and, allowing for the Volume contraction due to the temperature difference between the experiments, justifies the restraints applied in the structure calculation (Zn-S and Zn-N distances of 2.3 A and 2.0 A, respectively).

Trimethylsilyl- and trimethylstannyldimethylphosphane--convenient and versatile reagents for the synthesis of polyfluoroaryldimethylphosphanes.

Abstract: Trimethylsilyldimethylphosphane (Me3SiPMe2) and the corresponding tin compound (Me3SnPMe2) were used as reagents for the substitution of fluorine by the Me2P group in polyfluoroarenes C6F5X (X = F, H, Cl, CF3) and C5NF5. The reactions occur even under mild conditions (T = 0-20 C), either in benzene or without solvent, to give as a rule 4-X-1-(dimethylphosphano)tetrafluorobenzenes (XC6F4PMe2, 1-4) and 4-(dimethylphosphano)tetrafluoropyridine (C5NF4PMe2, 5), respectively, in yields between 75 and 95%. In the case of C6F6, double substitution is also observed, which affords 1,4-bis(dimethylphosphano)tetrafluorobenzene (6). A very efficient route to the compounds XC6F4PMe2 (X = F, H, Cl, CF3) and C5NF4PMe2 was developed as a one-pot reaction of the corresponding fluoroarenes with tetramethyldiphosphane (P2Me4) and trimethyltin hydride (Me3SnH) at moderate temperatures. This process was tested for C6F6 and perfluorobiphenyl which gave C6F5PMe2 (1) and 4,4'-bis(dimethylphosphano)octafluorobiphenyl (7), respectively. The results, which included kinetic measurements that used the intensities of the 31P signals, revealed the influence of the substrate type on the rate of reaction in the sequence: C5NF5>C6F5CF3> C6F5Cl, C6F5PMe2>C6F5H>C6F6>> C6H5F. Ab initio calculations were carried out on the model reactions of pentafluoropyridine with silylphosphane, phosphane or phosphide to discriminate between possible reaction mechanisms. The novel phosphanes were characterised by spectroscopic investigations (NMR, MS), by preparation of the related thiophosphanes ArFP(=S)Me2 (8-14), their spectroscopic and analytic data and single crystal X-ray diffraction studies on five of these derivatives.

Notizen: Thiogermanate mit adamantanartigen Ge4S104⊖-Ionen / Thiogermanates with Adamantane-Like Ge4S104⊖ Ions

Abstract: Neben dem einfachen tetraedrischen GeS44ö-Ion (vgl. z. B. 1. c . 1 _ 5 ) ist bisher das aus wäßriger Lösung dargestellte Ge2S649 als definiertes Thioanion des Germaniums charakterisiert worden4. Ge2S640 besteht aus zwei kantenverknüpften Tetraedern und stellt formal einen Ausschnitt aus der Kettenstruktur des SiS2 dar. Sowohl aus Lösung als auch nach Hochtemperaturmethoden sind Thiogermanate (bzw. ternäre Sulfide) mit der formalen Zusammensetzung Me2IGe2S5( -x H20) und MenGe2S5 isoliert worden, über deren exakte Darstellungsbedingungen und Einheitlichkeit z. T. noch keine Klarheit besteht und deren Strukturen unbekannt sind 6. Wir untersuchten die Darstellungsmöglichkeiten der Alkalithiogermanate dieser Stöchiometrie aus wäßriger Lösung und erhielten nach folgender einfacher Methode reproduzierbar wasserhaltige, kristalline Salze in hoher Ausbeute: GeS2 wird bis zur Sättigung unter leichtem Erwärmen in einer möglichst konzentrierten wäßrigen Lösung von polysulfid-freiem Alkalisulfid (Na, K, Rb oder Cs) aufgelöst. Dabei stellt sich ein pH-Wert von 6 — 7 ein. Aus der filtrierten, farblosen Lösung kristallisieren die leichtlöslichen, wasserhaltigen Salze beim Stehen über P4O10 aus. Das im festen Zustand stabilste und wasserärmste Cs-Salz wurde durch eine vollständige Röntgenstrukturanalyse und Schwingungsspektren als Cs4Ge4S104 H20 charakterisiert. Das Thiogermanat enthält isolierte Ge4Slo40-Ionen (Abb. 1) mit einem für anorganische Ionen bisher nicht beobachteten adamantan-analogen Gerüst. Die Struktur entspricht der des molekularen P4O10, des P4S10 und der alkylsubstituierten Verbindung Ge4S6(CH3)4 7. Bemerkenswert ist, daß die GeS4-Tetraeder im Ge4S 104°-Ion im Gegensatz zum Ge2S64° über Ecken verknüpft sind, daß also in der Reihe der formal polymerhomologen Ionen (GenSn + 2)40 kein einheitliches Strukturprinzip bestimmend ist. Ge4Slo40 ist in diesem Sinne ein erster Kondensationsschritt vom GeS440 zum hochpolymeren GeS2 . Das Ge4S104e-Ion ist in der Struktur nur unwesentlich (aber signifikant) verzerrt und hat fast ideale TdSymmetrie. Die Brücken-Ge-S-Bindungslängen variieren zwischen 2,184 und 2,268 Ä, diejenigen der endständigen Bindungen zwischen 2,104 und 2,126 Ä (o ~ 0,010 Ä). Die Mittelwerte der chemisch äquivalenten Bindungslängen und -winkel (Extremwerte 106,9 und 111,4°) sind in der Abb. 1 angegeben.

Tripodal Ligands: Design of Distorted Coordination Polyhedra in Biomimetic Metal Complexes. Crystal structures of [Zn(SCN)(ntb)](SCN) · iPrpOH and [Fe(acac)(ntb)](ClO4)2 · 2CH2Cl2 · iPrpOH, ntb = N‐tris(2‐benzimidazolylmethyl)amine

Abstract: The tripodal ligand N-tris(2-benzimidazolylmethyl)-amine (ntb) was used for the preparation of zinc(II) and iron(III) complexes, [Zn(SCN)(ntb)](SCN) · iPrpOH (1) and [Fe(acac)(ntb)](ClO4)2 · 2CH2Cl2 · iPrpOH (2). 1 has a highly distorted trigonal-bipyramidal ZnN5 coordination geometry. The donor atoms are nitrogens of one amine, three benzimidazoles and one SCN−. A striking feature of the complex is the length of the ZnNamine bond of 2.539(6)A. The octahedral N4O2 coordination sphere of the iron in 2 is less distorted than that of the zinc in 1. The metal is surrounded by an amine and three benzimidazole nitrogens of the ligand and two oxygens of the bidentate acetylacetonate co-ligand. The FeO bond lengths differ by about 0.1 A. As for the unusual long ZnN bond in 1 this is a result of a trans effect. 1 crystallizes in the space group P1 with: a = 9.530(1)A, b = 13.402(1)A, c = 13.578(2)A, α = 98.83(1), β = 95.19(1), γ = 101.21(1)°, Z = 2; 2 is also triclinic, space group P1, with: a = 9.875(6)A, b = 12.929(10)A, c = 18.635(15)A, α = 94.95(8)°, β = 101.01(6)°, γ = 111.09(4)°, Z = 2. Tripodliganden: Darstellung verzerrter Koordinationspolyeder in biomimetischen Metallkomplexen. Kristallstrukturen von [Zn(SCN)(ntb)](SCN) · iPrpOH und [Fe(acac)(ntb)](ClO4)2 · 2 CH2Cl2 · iPrpOH, ntb = N-Tris(2-benzimidazolylmethyl)amin Der Tripodligand N-Tris(2-benzimidazolylmethyl)amin (ntb) wurde zur Synthese eines Zink(II)- und eines Eisen(III)-Komplexes, [Zn(SCN)(ntb)](SCN) · iPrpOH (1) und [Fe(acac)(ntb)](ClO4)2 · 2 CH2Cl2 · iPrpOH (2), eingesetzt. Der Zinkkomplex hat eine stark verzerrte trigonal-bipyramidale Koordinationssphare. Die koordinierenden Atome sind ein Amin-N, drei Benzimidazol-N und ein SCN−-N-Atom. Auffallig hier ist der 2.539(6)A grose ZnNamin-Bindungsabstand. Das Koordinationspolyeder des Eisenkomplexes ist weniger stark verzerrt als das in 1 und wird von einem Amin- und drei Benzimidazol-Stickstoffatomen des Liganden sowie zwei Sauerstoffatomen des Acetylacetonats gebildet. Die FeO-Bindungslangen zeigen eine Differenz von ca. 0.1 A, die wie die ungewohnlich lange ZnN-Bindung durch einen Trans-Effekt verursacht wird. 1 kristallisiert triklin in der Raumgruppe P1 mit: a = 9.530(1), b = 13.402(1), c = 13.578(2)A, α = 98.83(1), β = 95.19(1), γ = 101.21(1)°, Z = 2; 2 ist ebenfalls triklin, P1, mit: a = 9.875(6), b = 12.929(10), c = 18.635(15)A, α = 94.95(8), β = 101.01(6), γ = 111.09(4)°, Z = 2.

The chemistry of graphene oxide

Abstract: The chemistry of graphene oxide is discussed in this critical review Particular emphasis is directed toward the synthesis of graphene oxide, as well as its structure Graphene oxide as a substrate for a variety of chemical transformations, including its reduction to graphene-like materials, is also discussed This review will be of value to synthetic chemists interested in this emerging field of materials science, as well as those investigating applications of graphene who would find a more thorough treatment of the chemistry of graphene oxide useful in understanding the scope and limitations of current approaches which utilize this material (91 references)

Phd by thesis

Abstract: Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

The hydrogen bond in the solid state.

Abstract: The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.

The transition metal dichalcogenides discussion and interpretation of the observed optical, electrical and structural properties

Abstract: The transition metal dichalcogenides are about 60 in number. Two-thirds of these assume layer structures. Crystals of such materials can be cleaved down to less than 1000 A and are then transparent in the region of direct band-to-band transitions. The transmission spectra of the family have been correlated group by group with the wide range of electrical and structural data available to yield useful working band models that are in accord with a molecular orbital approach. Several special topics have arisen; these include exciton screening, d-band formation, and the metal/insulator transition; also magnetism and superconductivity in such compounds. High pressure work seems to offer the possibility for testing the recent theory of excitonic insulators.

Multicopper Oxidases and Oxygenases

Abstract: Copper is an essential trace element in living systems, present in the parts per million concentration range. It is a key cofactor in a diverse array of biological oxidation-reduction reactions. These involve either outer-sphere electron transfer, as in the blue copper proteins and the Cu{sub A} site of cytochrome oxidase and nitrous oxide redutase, or inner-sphere electron transfer in the binding, activation, and reduction of dioxygen, superoxide, nitrite, and nitrous oxide. Copper sites have historically been divided into three classes based on their spectroscopic features, which reflect the geometric and electronic structure of the active site: type 1 (T1) or blue copper, type 2 (T2) or normal copper, and type 3 (T3) or coupled binuclear copper centers. 428 refs.