Synthesis and crystal structure of the palladium oxides NaPd3O4, Na2PdO3 and K3Pd2O4

NaPd₃O₄, Na₂PdO₃ and K₃Pd₂O₄ have been prepared by solid-state reaction of Na₂O₂ or KO₂ and PdO in sealed silica tubes. Crystal structures of the synthesized phases were refined by the Rietveld method from X-ray powder diffraction data. NaPd₃O₄ (space group Pm3¯n, a=5.64979(6) Å, Z=2) is isostructural to NaPt₃O₄. It consists of NaO₈ cubes and PdO₄ squares, corner linked into a three-dimensional framework where the planes of neighboring PdO₄ squares are perpendicular to each other. Na₂PdO₃ (space group C2/c, a=5.3857(1) Å, b=9.3297(1) Å, c=10.8136(2) Å, β=99.437(2)°, Z=8) belongs to the Li₂RuO₃-structure type, being the layered variant of the NaCl structure, where the layers of octahedral interstices filled with Na⁺ and Pd⁴⁺ cations alternate with Na₃ layers along the c-axis. Na₂PdO₃ exhibits a stacking disorder, detected by electron diffraction and Rietveld refinement. K₃Pd₂O₄, prepared for the first time, crystallizes in the orthorhombic space group Cmcm (a=6.1751(6) Å, b=9.1772(12) Å, c=11.3402(12) Å, Z=4). Its structure is composed of planar PdO₄ units connected via common edges to form parallel staggered PdO₂ strips, where potassium atoms are located between them. Magnetic susceptibility measurements of K₃Pd₂O₄ reveal a Curie-Weiss behavior in the temperature range above 80 K.     

A very large diversity space of synthetically accessible compounds for use with drug design programs

We have constructed a very large virtual diversity space containing more than 10¹³ chemical compounds. The diversity space is built from about 400 combinatorial libraries, which have been expanded by choosing sizeable collections of suitable R-groups that can be attached to each link point of their scaffolds. These R-group collections have been created by selecting reagents that have drug-like properties from catalogs of available chemicals. As members of known combinatorial libraries, the compounds in the diversity space are in general synthetically accessible and useful as potential drug leads. Hence, the diversity space can be used as a vast source of compounds by a de novo drug design program. For example, we have used such a program to generate inhibitors of HIV integrase enzyme that exhibited activity in the micromolar range.     

Role of resonances in building cross sections: Comparison between the Mittag–Leffler and the T‐matrix Green function expansion approaches

Peaks in collision cross sections are often interpreted as resonances. The complex dilation method, as well as other methods relying on analytic continuation of the scattering formalism, can be used to clarify whether these structures are true resonances in the sense that they are poles of the S‐matrix and the associated Green function. The performance of the Mittag–Leffler expansion and T‐matrix Green function expansion methods are formally and computationally compared. The two methods are applied to two model potentials. Eigenenergies, s‐wave residues, and cross sections are computed with both methods. The resonance contributions to the cross sections are further analyzed by removing the residue contributions from the Mittag–Leffler and Green function expansion sums, respectively. It is suggested that the contribution of a resonance to a cross section should be defined through its S‐matrix residue. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Polymerization dynamics of double-stranded biopolymers: chemical kinetic approach

The polymerization dynamics of double-stranded polymers, such as actin filaments, is investigated theoretically using simple chemical kinetic models that explicitly take into account some microscopic details of the polymer structure and the lateral interactions between the protofilaments. By considering all possible molecular configurations, the exact analytical expressions for the growth velocity and dispersion for two-stranded polymers are obtained in the case of the growing at only one end, and for the growth from both polymer ends. Exact theoretical calculations are compared with the predictions of approximate multilayer models that consider only a finite number of the most relevant polymer configurations. Our theoretical approach is applied to analyze the experimental data on the growth and fluctuations dynamics of individual single actin filaments.     

Spectroscopy, electrochemistry, and molecular orbital calculations of metal-free tetraazaporphyrin, -chlorin, -bacteriochlorin, and -isobacteriochlorin

Metal-free tetraazachlorin (TAC), -bacteriochlorin (TAB), and -isobacteriochlorin (TAiB) were characterized by electronic absorption, magnetic circular dichroism (MCD), fluorescence, and time-resolved ESR (TR-ESR) spectroscopy, and by cyclic voltammetry. The results are compared with those of metal-free tetraazaporphyrin (TAP). The potential difference DeltaE between the first oxidation and reduction couples decreases in the order TAP>TAiB>TAC>TAB. The splitting of both the Q and Soret bands decreases in the order TAB>TAC>TAP>TAiB. Corresponding to the split absorption bands, MCD spectra show a minus-to-plus pattern with increasing energy in both the Q and Soret regions, which suggests that the energy difference between the HOMO and second HOMO is larger than that between the LUMO and second LUMO. These spectroscopic properties and redox potentials were reproduced by molecular orbital calculations using the ZINDO/S Hamiltonian. The fluorescence quantum yields of the reduced species are much smaller than that of TAP. The zero-field splitting (ZFS) parameters D and E of the excited triplet states (T1) of these species decrease and increase, respectively, on going from TAP to TAC and further to TAB. The D and E values of TAiB are larger than those of the other species. The results are supported by the absence of interaction between the spin over reduced pyrrole moieties of the HOMO and over the LUMO, and by calculations of ZFS under a half-point-charge approximation.     

Finite element investigation of the ground states of the helium trimers 4He3 and 4He2–3He

A three‐dimensional finite element method is applied to the ground states of the symmetric and asymmetric atomic helium trimers ⁴He₃ and ⁴He₂–³He. Three different He–He interaction potentials of hard‐core nature were studied. Two extrapolation procedures based on the convergence properties of the finite element method are investigated. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Betaine 0.77‐perhydrate 0.23‐hydrate and common structural motifs in crystals of amino acid perhydrates

The title compound, betaine 0.77‐perhydrate 0.23‐hydrate, (CH₃)₃N⁺CH₂COO⁻·0.77H₂O₂·0.23H₂O, crystallizes in the orthorhombic noncentrosymmetric space group Pca2₁. Chiral molecules of hydrogen peroxide are positionally disordered with water molecules in a ratio of 0.77:0.23. Betaine, 2‐(trimethylazaniumyl)acetate, preserves its zwitterionic state, with a positively charged ammonium group and a negatively charged carboxylate group. The molecular conformation of betaine here differs from the conformations of both anhydrous betaine and its hydrate, mainly in the orientation of the carboxylate group with respect to the C—C—N skeleton. Hydrogen peroxide is linked via two hydrogen bonds to carboxylate groups, forming infinite chains along the crystallographic a axis, which are very similar to those in the crystal structure of betaine hydrate. The present work contributes to the understanding of the structure‐forming factors for amino acid perhydrates, which are presently attracting much attention. A correlation is suggested between the ratio of amino acid zwitterions and hydrogen peroxide in the unit cell and the structural motifs present in the crystal structures of all currently known amino acids perhydrates. This can help to classify the crystal structures of amino acid perhydrates and to design new crystal structures.