Copper—A “Modern” Bioelement

Copper is a bioessential element in biology with truly unique chemical characteristics in its two relevant oxidation states +I and +II. Significant progress has been made in recent years in the elucidation of the frequently surprising biochemistry of this trace element. Those advances were especially furthered through mutual stimulation involving results from biochemistry, molecular biology, and medicine on one hand and the synthesis as well as the structural and spectroscopic characterization of low molecular weight model complexes on the other. The most notable features of protein-bound active copper are its almost exclusive function in the metabolism of O₂ or N/O compounds (NO, N₂O) and its frequent association with oxidizing organic and inorganic radicals such as tyrosyl, semiquinones, superoxide, or nitrosyl. This unique biological role of copper can be rationalized given its chemical and assumed evolutionary background.     

Cover Picture: Trimeric Perfluoro‐ortho‐phenylenemercury: A Versatile Lewis Acidic Host (Chem. Eur. J. 21/2003)

The cover picture shows how trimeric perfluoro‐ortho‐phenylene mercury (center), one of the simplest trifunctional Lewis acidic hosts, interacts with organic molecules to afford various adducts. The planarity of this trinuclear complex as well as its overall polarizability compounded with relativistic effects at mercury permits the occurrence of noncovalent interactions and accounts for the tendency of this compound to form cofacial dimers as observed in the structure of the acetone adduct (top left). With a triply coordinated acetone molecule, the structure of this adduct also substantiates the cooperative effects that arise from the proximity and accessibility of the mercury centers. The complexation of arenes, such as benzene (bottom left) and naphthalene (bottom right), also occurs and leads to the formation of binary stacks in which the arene establishes multiple linkages with the mercury centers of the trifunctional Lewis acids. In addition to displaying unusual coordination environment, the arene units present in those stacks exhibit remarkable phosphorescent properties. For more details, see the paper by F. P. Gabbaï, R. E. Taylor, and M. R. Haneline on p. 5188 ff.     

Basis Set Orbital Relaxation in Atomic and Molecular Hydrogen Systems

Orbital relaxation (OR) amounts to variation of the orbital exponents in hydrogen molecules and ions relative to the exponents of the isolated atom; it is represented as the sum of the one- and two-center contributions depending on the effective atomic charge and on the presence of other atoms in the molecule. The procedure for isolating the contributions of the exponent includes treatment of the OR of hydrogen in a special set of neutral and charged atoms and molecules with certain multiplicities of their electronic states. Within the framework of the spin-unrestricted Hartree-Fock method, we found and discussed the optimal values of the exponents of the basis orbitals of hydrogen atoms and molecules using the minimal split valence-shell basis set, the basis set that includes the polarization function, and the expanded set of grouped natural orbitals. A simple energy model is suggested for OR. Expressions are derived for evaluating the exponents of the relaxed orbitals in hydrogen-containing systems.Original Russian Text Copyright © 2004 by A. I. Ermakov, A. E. Merkulov, A. A. Svechnikova, and V. V. Belousov__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 973–978, November–December, 2004.     

Dynamic chirality: keen selection in the face of stereochemical diversity in mechanically bonded compounds

The template-directed syntheses, employing bisparaphenylene-[34]crown-10 (BPP34C10), 1,5-dinaphthoparaphenylene-[36]crown-10 (1/5NPPP36C10), and 1,5-dinaphtho-[38]crown-10 (1/5DNP38C10) as templates, of three [2]catenanes, whereby one of the two bipyridinium units in cyclobis(paraquat-p-phenylene) is replaced by a bipicolinium unit, are described. The crude reaction mixtures comprising the [2]catenanes all contain slightly more of the homologous [3]catenanes, wherein a "dimeric" octacationic cyclophane has the crown ether macrocycles encircling the alternating bipyridinium units with the bipicolinium units completely unfettered. X-ray crystallography, performed on all three [2]catenanes and two of the three [3]catenanes reveals co-conformational and stereochemical preferences that are stark and pronounced. Both the [3]catenanes crystallize as mixtures of diastereoisomers on account of the axial chirality associated with the picolinium units in the solid state. Dynamic (1)H NMR spectroscopy is employed to probe in solution the relative energy barriers for rotations by the phenylene and pyridinium rings in the tetracationic cyclophane component of the [2]catenanes. Where there are co-conformational changes that are stereochemically "allowed", crown ether circumrotation and rocking processes are also investigated for the relative rates of their occurrence. The outcome is one whereby the three [2]catenanes containing BPP34C10, 1/5NPPP36C10, and 1/5DNP38C10 exist as one major enantiomeric pair of diastereoisomers amongst two, four, and eight diastereoisomeric pairs of enantiomers, respectively. The diastereoisomerism is a consequence of the presence of axial chirality together with helical and/or planar chirality in the same interlocked molecule. These [2]catenanes constitute a rich reserve of new stereochemical types that might be tapped for their switching and mechanical properties.     

Reaction of Tetracopper(I)-Phosphonitocavitand with PhSeSiMe3: Synthesis and Structure of a Polyanionic Cluster [pyH]6[(CuCl)9(μ3-SePh)5(μ4-SePh)]

Treatment of tetracopper(I)-phosphonitocavitand [1·Cu₄(μ-Cl)₄(μ₄-Cl)] (2) (1 = tetraphosphonitocavitand [rccc-2,8,14,20-tetrakis-(iso-butyl)-phosphonitocavitand (C₄₄H₄₈O₈P₄Ph₄)]) with PhSeSiMe₃ in THF at low temperature afforded a novel polyanionic cluster [pyH]₆[(CuCl)₉(μ₃-SePh)₅(μ₄-SePh)] (4) as a major product along with a new tetracopper(I)-phosphonitocavitand (3) with a centered μ₃-Cl. Molecular structure of anionic cluster in 4 consists of six PhSe⁻ bridging ligands containing five μ₃-SePh and one exceptional μ₄-SePh bridging nine copper atoms, of which eight copper atoms have trigonal coordination geometry and the other has distorted tetrahedral geometry. Dedicated to Professor Han-Qin Liu on the occasion of his 70th birthday.     

Chemical Reactions and Kinetics of the Carbon Monoxide Coupling in the Presence of

The chemical reactions and kinetics of the catalytic coupling reaction of carbon monoxide to diethyl oxalate were studied in the presence of hydrogen over a supported palladium catalyst in the gaseous phase at the typical coupling reaction conditions. The experiments were performed in a continuous flow fixed-bed reactor. The results indicated that hydrogen only reacts with ethyl nitrite to form ethanol, and kinetic studies revealed that the rate-determining step is the surface reaction of adsorbed hydrogen and the ethoxy radical (EtO-). A kinetic model is proposed and a comparison of the observed and calculated conversions showed that the rate expressions are of rather high confidence.     

Some thermodynamic aspects of highT c superconductors

Thermochemical and thermodynamical properties of HTSC phases are reviewed for the Y-Ba-Cu-O system and also presented for the newly calculated Bi-Sr-Cu-O system stressing out stoichiometric and phenomenological viewpoints. Simulated data are listed for (H ₂₉₈ ^o -H _o ^o , phase transformation temperatures, standard entropies, standard enthalpies of formation, heat capacities in crystalline phase, etc. Pseudobinary phase diagrams are treated showing the effect of oxygen partial pressure particularly illustrated on the (Sr, Bi, Ba)-Cu-O system.The work was carried out under the project No. A 2010532 supported by the Grant Agency of Academy of Sciences of the Czech Republic and the grant No. 104/97/0589 financed by the Grant Agency of the Czech Republic.     

Factor Xa: Simulation studies with an eye to inhibitor design

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 Å resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.     

Interface motion in a two-dimensional Ising model with a field

We determine by Monte Carlo simulations the width of an interface between the stable phase and the metastable phase in a two-dimensional Ising model with a magnetic field, in the case of nonconversed order parameter (Glauber dynamics). At zero temperature, the width increases ast with–1/3, as predicted by earlier theories. As temperature increases, the value of the effective exponent that we measure decreases toward the value 1/4, which is the value in the absence of magnetic field.