Computer simulation of the binding of quinocarcin to DNA. Prediction of mode of action and absolute configuration

Summary Computer-based models were derived for the covalent and noncovalent binding of the antitumor antibiotic quinocarcin to a representative DNA segment, d(ATGCAT)₂. They showed that a mode of action, involving opening of the oxazolidine ring to give an iminium ion, followed by initial noncovalent binding in the minor groove and subsequent alkylation of the 2-amino group of guanine, was rational and attended by favorable interaction energies in each step. The best model had the aryl ring of quinocarcin lying in the 3 direction from the covalent binding site and anR configuration at the carbon involved in covalent bond formation. It also showed that the preferred absolute configuration for quinocarcin was the reverse of that arbitrarily assigned in the literature.     

The structure of isomeric anthraquinonesulfonic acids

The ultraviolet and infrared spectra of the isomeric anthraquinonesulfonic acids in the solid state and in aqueous and sulfuric acid solutions have been studied. It has been established that interaction takes place between the C=O group and the SO₂OH group in the - and , -sulfonic acids. Possible mechanisms of this interaction for the ionized and covalent compounds have been discussed. It has been shown that all the sulfonic acids retain the anthraquinonoid structure at all sulfuric acid concentrations. It has been concluded that unlike anthraquinone itself, anthraquinonesulfonic acids do not undergo protonation in concentrated sulfuric acid, but form associates with the solvent.     

K3Na26In48: An Intermetallic Phase with Large Pseudo-icosahedral Clusters and a Na46 Clathrate-I Network Enveloping a Covalent [In12] Cluster Framework

K₃Na₂₆In₄₈ was synthesized from the elements in sealed niobium ampoules (melted at 873 K; annealed at 573 K). The compound forms brittle crystals with silver metallic lustre, behaves as a metallic conductor, and is very sensitive to air and moisture. The crystal structure of K₃Na₂₆In₄₈ (cubic; space group Pm3 n,No. 223; a = 16.046(2) Å; Z = 2; Pearson symbol cP154) contains two empty icosahedral In and six hexagonal antiprismatic In indium clusters per unit cell. The latter are centered by Na atoms. All In₁₂ clusters are interconnected by 12 exo-bonds forming a covalent 3 D network (In—In = 2.912—3.149 Å). The remaining Na atoms form a Na₄₆ 3 D-network of the clathrate-I type with (2 + 6) cages, enveloping the In₁₂ clusters network. This novel structure can be regarded as a filled derivative of the clathrate-I structure: . The potassium atoms link the filled [NaIn] clusters to 1 D columns, and also form (6,4) net of the NbO type with Na atoms at bridging positions. The whole structure can also be described as a bcc packing of huge condensed A₁₂₂ clusters (16 Å diameter) which have nearly icosahedral symmetry and consist of several atomic shells. The bonding as well as the structural relationships to other phases are discussed in detail.     

Structural features and the nature of the hydrogen bond in the enol form of α-diphenylphosphoryl-α-acetylacetonitrile based on X-ray diffraction data

It has been established by X-ray structural analysis that pure -diphenylphosphoryl--acetylacetonitrile exists in the enol form (aZ isomer). In crystals, a strong intramolecular P=O...H...O hydrogen bond is formed; the O...O distance is 2.551 Å. It has been demonstrated that the H atom is characterized by a high lability along the hydrogen bond, which exhibits a covalent component in the H...O region.Deceased.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1520–1524, August, 1995.The X-ray structural study was supported by the American Crystallography Association and the International Science Foundation (Grant No. M1F000).     

Tensile yield of isotactic polypropylene in terms of a lamellar‐cluster model

In this study, the structural factors controlling the yield in isotactic polypropylene materials were theoretically investigated. To describe the yielding behavior of spherulitic polypropylenes, we introduced a new structural unit, lamellar clusters, which are several stacked lamellae bound by tie molecules. It was shown that tie molecules between adjacent lamellar clusters produce a concentrated load acting on the cluster surface, leading to the bending deformation of the lamellar clusters. The yielding behavior can be explained if one assumes that the disintegration of the lamellar clusters occurs when the elastic‐strain energy stored by the bending deformation reaches a critical value. By applying the fracture theory of composites to a system consisting of lamellar clusters and tie molecules, we found the yield stress σ_y to be proportional to , in which E_Y is the Young's modulus and U_y is the yield energy. The proportional coefficient between σ_y and depends only on the cluster size and tie‐molecule density, so this proportionality is expected to be true for other spherulitic semicrystalline polymers such as polyethylenes, being independent of temperature and tensile rate. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1037–1044, 2000     

Molecular and crystal structures of ruthenium and osmium arene clusters

The molecular and crystal structures of a number of ruthenium and osmium clusters of nuclearity between three and six containing arene fragments such as C₆H₆, C₆H₃Me₃, C₆H₄Me₂ and C₆H₅Me have been investigated. Attention has been focused on the relationship between the terminal ( ⁶-coordination) and face-capping ( ₃: ²: ²: ²-coordination) bonding modes. Empirical packing potential energy calculations have been employed to investigate the intermolecular organization in the crystal. It has been shown that the arene fragments in mono-arene clusters form ribbons, while in bis-arene clusters graphitic-like interactions throughout the crystal are established. The factors controlling the ease of arene reorientational motion in the solid state has also been investigated in relation to the shape, size and geometry of the molecules and of their interlocking modes.     

A Topological Study of the Ferromagnetic “No-Pair Bonding” in Maximum-Spin Lithium clusters: n+1Li n (n=2–6)

The nature of the bonding between lithium atoms, in low-spin and maximum-spin clusters, was investigated using the topological electron localization function (ELF) approach. The maximum-spin clusters are especially intriguing since their bonding is sustained without having even a single electron pair! Hence this type of bonding had been called “no-pair ferromagnetic-bonding” [Danovich, Wu, Shaik J Am Chem Soc 121:3165 (1999); Glokhovtsev, Schleyer Isr J Chem 33: 455 (1993); de Visser, Danovich, Wu, Shaik J Phys Chem A 106:4961 (2002)]. The following conclusions were reached in the study: (a) In the ground state of Li _n , covalent bonding between Li atoms is accounted by the presence of the disynaptic valence basins, which exhibit a significant degree of inter-basin delocalization. (b) Except for the ³Li₂ case, the valence basins of all maximum-spin clusters are populated by unpaired electrons. The valence basins are located off Li–Li axis (or Li–Li–Li plane), so that their spatial distribution minimizes the mutual Pauli repulsion and screens the electrostatic repulsion between the Li cores. The inter-basin delocalization is rather high, thereby indicating that the unpaired electrons are virtually delocalized over all the valence basins. (c) The ELF analysis shows that Li atoms in the low-spin clusters are bonded by “two-center two-electron” and “three-center two-electron” bonds. (d) In the maximum-spin species, bonding is sustained by “two-center one-electron” and “three-center one-electron” bonds. The latter picture is complementary to the valence bond picture [Danovich, Wu, Shaik J Am Chem Soc 121 3165 (1999); de Visser, Danovich, Wu, Shaik J Phys Chem A 106: 4961 (2002)], in which the bicentric ferromagnetic-bonding is delocalized over all the short Li–Li contacts, by the mixing of the ionic structures and other nonredundant structures into the repulsive high-spin covalent structure in which all the electrons populate the 2s atomic orbitals, i.e., the configuration. In such a manner bonding can be sustained from “purely ferromagnetic interactions” without electron pairing.Dedicated to Jean-Paul Malrieu, a friend and a poet-scientist     

Embedding frequencies of trees

A graph is said to be embedded in a graph if is isomorphic to a subgraph of . The embedding frequency for in ,N( , ), is the number of different subgraphs of to which is isomorphic. We use a computer program to calculate the embedding frequencies of subtrees within trees. We computeN(, ) for trees through 10 vertices and present the results in tabular form. When trees are partially ordered by valence class, their subtrees lie in corresponding order; we give a formal proof of this subtree embedding property. The structure of the embedding relation is exhibited in a topological picture of the zeta function showing the non-zero values ofN(, ).     

Interpreting magic-number and evaporation effects in cluster size distributions

The Smoluchowski equations describe the coalescence of clusters to form larger clusters. If the kernels or rate constants in these equations are homogeneous, meaning thatK _{j, k} = ² K _jk (wherej andk are cluster sizes), it can be shown that the populationsn _k approachAk ^a e - ^bk for largek and large time, where the constantsa andb depend on the homogeneity parameter. Deviations of observed populations from this formula may be ascribed to magic-number and/or evaporation effects on the kernels. By integrating the Smoluchowski equations numerically for various choices of the kernels, we derive population distributions and show the effects of magic-number clusters and evaporation on the population distribution. Various methods are used to extract the value of, in order to determine the best way to extract the underlying value of from experimental data. Experimental populations for sodium metal clusters are then analyzed according to the same procedure, to extract the homogeneity parameter and explain the patterns in the population distribution.     

Similarity and complexity of the shapes of square-cell configurations

Summary An equivalence relation on square-cell configurations, which we call animals, is formulated precisely, using the similarity criterion of seeing parts of the shape of the animal from its interior, and an operation called squashing, leading to a smaller animal. It is noted that there is a unique smallest animal in each resulting equivalence class, called the canonical animal of its class. It is proposed that the number of cells in a canonical animalA serves as a measure of complexity of any animal similar toA. The formulation of the canonical animal is suggested as a tool for characterizing shapes of monolayer clusters of adsorbed molecules on square lattices, a problem of importance in chemical catalysis.     

Atomic bonding of neutral and cationic Mn clusters

By using the spin-polarized DV-X-LCAO method, electronic states of neutral and cationic Mn _N clusters (N=25) are calculated to study atomic bonding of Mn clusters. For the neutral Mn₂ cluster, the equilibrium interatomic distance is much larger than that of the bulk crystal. The 3d-derived states are nearly half-filled, and the 4s-derived states are almost fully occupied,i.e. the electronic configuration is close to that of the isolated atom. These indicate that the Mn₂ cluster is bound by the van der Waals force. The same situation is true for the larger neutral clusters while the equilibrium interatomic distance becomes smaller and thes-d mixing becomes larger. For the cationic clusters, the behaviors tend to become metallic. The equilibrium interatomic distances are smaller and thes-d mixings are larger than those of the corresponding neutral clusters. However, the Mn ₂ ⁺ and Mn ₄ ⁺ clusters still remain the van der Waals characters. Contrary to these clusters, the Mn ₅ ⁺ cluster, whose interatomic distance is smaller than that of the bulk crystal, shows strong metallic bonding. These results seem to correspond to the magic number observed on the mass spectroscopy of cationic Mn clusters.     

On expectation value calculations of one-electron properties using the coupled cluster wave functions

The ability of various approximate coupled cluster (CC) methods to provide accurate first-order one-electron properties calculated as expectation values is theoretically analysed and computationally examined for BH and CO. For actual calculations the infinite number of terms of the expectation value expansion (O=¦exp (T ⁺)O exp (T)¦_c) was truncated so that T ₁ T ₂, T ₃, and (1/2) T ₂T₂ clusters were retained on both sides of O. The role of individual clusters is carefully discussed. Inclusion of T ₁, is unavoidable, but if triples are essential in the energy evaluation, they may play an even more important role in the property expansion, as shown in the case of CO. It is shown that the CC wave function, which is exact to second order, effectively satisfies the Hellmann-Feynman theorem.     

Electronegativity equalization and the electronic structure of polyhedral clusters of main-group atoms

The concept of the equalization of atomic electronegativities accompanving molecule formation is applied to a study of the electronic structure of polyhedral clusters of main-group atoms such as Ge, Sn, Pb, Tl, and Bi. Emphasis is placed upon charged clusters such as Sn_9?x Pb(x = 0 → 9), Sn_9-xGe, Sn_8?xPb_x Tl^5?, Sn₂Bi, SnTe, etc. The role of the relativistic spin-orbit splitting of an np shell into np_1/2 and np_3/2 subshells in modifying atomic and hence molecular electronegativities is discussed. Correlations are made between calculated charge distributions and observed¹⁹⁹ Sn NMR chemical shifts for clusters of a given size and charge. It is concluded that a useful picture of charge distributions in these clusters may be obtained from electronegativity equalization considerations.     

Density functional theory study of geometry and stability of small Zrn (n = 2–10) clusters

Geometric structures, electronic properties, and stabilities of small Zr_n and Zr (n = 2–10) clusters have been investigated using density functional theory with effective core potential LanL2DZ basis set. For both neutral and charged systems, several isomers and different multiplicities were studied to determine the lowest energy structures. Many most stable states with high symmetry were found for small Zr_n clusters. The most stable structures and symmetries of Zr clusters are the same as the neutral ones except n = 4 and 7. We found that the clusters with n > 3 possess highly compact structures. The clusters are inclined to form the caged‐liked geometry containing pentagonal structures for n > 8, which is in favor of energy. From the formation energy and second‐order energy difference, we obtained that 2‐, 5‐, 7‐atoms of neutral and 4‐, 7‐atoms cationic clusters are the magic numbers. Furthermore, the highest occupied molecular orbital‐lowest unoccupied molecular orbital gaps display that the Zr₃, Zr₆, Zr, and Zr are more stable in chemical stability. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Density functional study of hydrogen adsorption and dissociation on small Pdn (n = 1–7) clusters

Density functional theory has been performed to investigate the interaction of H₂ and Pd_n clusters (n = 1–7). The local minima configurations for different H₂ molecule approach modes towards Pd_n clusters are presented. Our results show that in some cases H₂ is physically adsorbed around Pd atom, and in other cases H₂ is dissociated to be H atoms. Except for PdH2, Pd_n clusters with H atoms dissociatively adsorbed are most stable. For these most stable PdnH2 clusters (n  2), the binding energy of hydrogen atom decreases as the number of Pd atom increases until n = 4, and when n  4, the binding energy almost keeps constant with the H atoms bound sites changing from Pd–Pd bonds to Pd triangle planes. Besides, the adsorption of H₂ on other low-lying isomers of Pd_n clusters is also discussed.     

Lumineszierende Cu(I)- und Ag(I)-Cluster mit Thionoliganden

Zusammenfassung Cu(I) bildet mit zahlreichen nicht lumineszierenden Thionoliganden (N-monosubstituierten N-Sulfonylthioharnstoffen, N,N-Dialkyl-N-phenylthioharnstoffen und N,N-Dialkylmonothiocarbamaten) rot lumineszierende oktaedrische Cluster (CuL)₆. Die Lumineszenz tritt sowohl im Festzustand als auch in Lösungen auf. Abklingzeiten von 10^–5s deuten auf kurzlebige Phosphoreszenz hin. Der Einfluß verschiedener Strukturelemente auf die Lage der Emissionsmaxima wird diskutiert. Dabei bewirken Veränderungen in der Metall-Ligand-Koordination die stärkste Verschiebung der Lumineszenzbanden. Tetraedrische (CuL)₄-Cluster mit den obigen Thionoliganden zeigen keine Lumineszenz. Generelle Unterschiede in der Struktur oktaedrischer und tetraedrischer Cluster werden diskutiert.Ag(I) bildet nur mit N-Alkyl-N-sulfonylthioharnstoffen lumineszierende Cluster (AgL)₆. Die Lumineszenz ist im Gegensatz zu den Cu-Clustern auf den Festzustand beschränkt.

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Luminescent Cu(I) and Ag(I) clusters with thiono ligands

Summary Octahedrical (CuL)₆ clusters with several non luminescent thiono ligands (N-monosubstituted N-sulfonylthioureas, N,N-dialkyl-N-phenylthioureas and N,N-dialkylmonothiocarbamates) show red luminescence in the solid state and in solution. The luminescence lifetimes of 10^–5s are typical of short lived phosphorescence. The emission bands are affected by structural variation of the ligand. Changes of the coordination bonds cause the strongest shifts of the luminescence maxima. Tetrahedrical (CuL)₄ clusters with the same thiono ligands are not luminescent. General structural differences between octahedral and tetrahedral clusters are discussed.(AgL)₆ clusters are only luminescent in the solid state and if the ligand is a N-monosubstituted N-sulfonylthiourea

     

On the behaviour of small clusters near the spinodal decomposition

The canonical average of the Boltzmann factor of the interaction potential, as measured by a test particle, is shown to be equal to the inverse of the fraction of the average number of 1-particle Mayer clusters. The potential distribution theory is used to derive an analytic expression for a mean number of small clusters 1≤n<N, in anN-particle system) in the mean-field expression. Near the spinodal density, the average number of small clusters undergo a sharp change. Computation of pressure shows that only the first four clusters produce surprisingly good agreement with known pressure even beyond the spinodal density. Contribution No. 439 from the Solid State and Structural Chemistry Unit     

Cation distribution of the cochlea wall (Stria vascularis)

Summary It was possible to maintain the differentiated structure of inner ear tissues by freezing in supercooled propane, freeze-drying under special conditions and embedding the tissue in a low viscosity resin. Using LAMMA we were able to measure intracellular ion concentration and concentration gradients in the soft tissues such as muscle and stria vascularis specimens. The preliminary results demonstrate that the distribution of cations in the lateral wall of the cochlear duct is not uniform. The K/Na ratio in the basal cells was significantly higher (121) than in the spiral ligament and middle part of the stria vascularis (71). Changes of such concentration ratios recorded after anoxia suggest that an energy dependent active transport mechanism must exist in the stria vascularis.

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Kationenverteilung in der Schneckengangwand des Ohres (Stria vascularis)

     

Synthesis and Characterization of Chromium(III), Molybdenum(III), Ruthenium(III) and Osmium(III) Complexes with N2O2–Schiff Bases of 2-Hydroxy-1-Naphthaldimines

Monomolybdenum, monochromium, triosmium and triruthenium clusters, containing weakly coordinated ligands, are valuable starting materials for the preparation of a wide variety of compounds because of the ease with which these ligands can be displaced by another substrate under mild conditions. Four widely used complexes of this type are Mo(CO)₆, Cr(CO)₆, Os₃(CO)₁₂ and Ru₃(CO)₁₂ respectively. These complexes react with 2-hydroxy-1-naphthaldimines to give octahedral complexes which are characterized by elemental analyses, i.r. and u.v.–vis. spectra, molar conductances, d.t.a. and t.g.a. analyses, cyclic voltammetry, magnetic and e.s.r. measurements. The molar conductances in DMF solution indicate that the complexes are non-ionic. The i.r. spectra of complexes (3), (7) and (10) show (CO) bands due to bonded CO groups, however complexes (6) and (13) show (CO) bands due to bonded, bridged and terminal CO groups. The g ₁₁-values of the complexes indicate that they have covalent bond character. Also, the electrochemical reduction of the complexes has been discussed.