Ab initio mo study on base stacking: Adenine-adenine interaction in single-stranded polyadenylic acid (Poly A)

The interaction energy for base stacking in single-stranded poly A is calculated by an ab initio MO method. The calculated value agrees well with the observed stacking enthalpy. Dispersion and charge transfer interactions are the main factors stabilizing the polynucleotide; the contribution of the former is dominant.     

Synthesis and Characterization of Ml2-Intercalated Bi-2212 Cuprates (M=Mn,Fe, Co,Cu, Zn)

Abstract

A series of new layered cuprates with the composition MI_2+xBi₂Sr₂CaCu₂O_8+y (x=0.6–0.9; M=Mn, Fe, Co, Cu, Zn) have been synthesized by the reaction of Bi₂Sr₂CaCu₂O₈ with each transition metal under an atmosphere of iodine at 400°C. The new cuprates, lamellar in shape, are crystallized in a tetragonal unit cell with the lattice parameters of a = 5.393–5.402 Å and c = 43.32–43.96 Å. A structure model for these cuprates are proposed in which the monoiodide anions are intercalated in the Bi₂O₂ layer to form a bilayer accompanying 3d metal cations. All of the intercalated cuprates are non-superconducting to be as high as 0.74–2.52 MΩ · cm in resistivity at room temperature.     

Ecosystems perspective on financial networks: Diagnostic tools

The world economy consists of highly interconnected and interdependent commercial and financial networks. Here, we develop temporal and structural network tools to analyze the state of the economy and the financial markets. Our analysis indicates that a strong clustering can be a warning sign. Reduction in diversity, which was an essential aspect of the dynamics surrounding the financial markets crisis of 2008, is seen as a key emergent feature arising naturally from the evolutionary and adaptive dynamics inherent to the financial markets. Similarly, collusion amongst construction firms in a number of regions in Japan in the 2000s can be identified with the formation of clusters of anomalous highly connected companies. © 2013 Wiley Periodicals, Inc. Complexity 19: 22–36, 2013     

Discussion of “Virtual age,is it real?”

In this note, some point of views on virtual ages are presented in terms of the discussion paper written by Finkelstein and Cha, which include generalized stochastic order‐based virtual ages, system‐level virtual ages, virtual ages in Weibull distribution and repair degrees with virtual ages. Finally, some possible future researches on virtual ages are described.     

Synthesis of ethyl 5-cyano-6-hydroxy-2-methyl-4-(1-naphthyl)-nicotinate

A novel ethyl 5-cyano-6-hydroxy-2-methyl-4-(1-naphthyl)-nicotinate is successfully synthesized and the structure is determined by XRD, GC-MS analysis, element analysis and NMR spectroscopic in detail. A reaction mechanism for the reaction is proposed.     

Kinetic investigations of the process of encapsulation of small hydrocarbons into a cavitand-porphyrin

Exchange of guest molecules into capsule shaped host molecules is the most fundamental process in host-guest chemistry. Several examples of quantitative measurements of guest exchange rates have been reported. However, there have been no reports on the activation energies of these processes. A molecule known as cavitand-porphyrin (H2CP) has been reported to have a flexible host structure capable of facilitating moderate guest exchange rates suitable for kinetic measurements of the guest exchange process with 1H NMR. In this article, various kinetic and thermodynamic parameters related to the process of encapsulation of small hydrocarbons into H2CP in CDCl3 solution were determined by 2D exchange spectroscopy (EXSY): association and dissociation rate constants (k(ass) = 320 M-1 s-1, k(diss) = 1.4 s-1 for methane at 25 degrees C), the corresponding activation energies (E(a,ass) = 27 kJ.mol-1, E(a,diss) = 58 kJ.mol-1), and thermodynamic parameters for each process (DeltaG++(ass) = 59 kJ.mol-1, DeltaG++(diss) = 72 kJ.mol-1, DeltaH++(ass) = 25 kJ.mol-1, DeltaH++(diss) = 55 kJ.mol-1, DeltaS++(ass) = -113 J.K-1.mol-1, and DeltaH++(diss) = 58 J.K-1.mol-1 for methane). The thermodynamic parameters (DeltaG degrees = -13 kJ.mol-1, DeltaH degrees = -31 kJ.mol-1, DeltaS degrees = -60 J.K-1.mol-1 for methane) for this encapsulation equilibrium determined by EXSY were comparable to those for methane determined by 1D 1H NMR titration (DeltaG degrees = -11 kJ.mol-1, DeltaH degrees = -33 kJ.mol-1, DeltaS degrees = -75 J.K-1.mol-1 for methane). In addition, the structure of the methane encapsulation process was revealed by ab initio MO calculations. The activation energies for methane association/dissociation were estimated from MP2 calculations (E(a,ass) = 58.3 kJ.mol-1, E(a,diss) = 89.1 kJ.mol-1, and DeltaH degrees = -30.8 kJ.mol-1). These values are in accord with the experimentally determined values. The observed guest exchange rates and energies are compared with the corresponding values of various reported capsule-shaped hosts.     

Ab initio ONIOM-molecular dynamics (MD) study on the deamination reaction by cytidine deaminase

We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase by calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determining step is the release of the NH3 molecule.     

An accurate numerical multicenter integration for molecular orbital theory

A powerful and accurate numerical three‐dimensional integration scheme was developed especially for molecular orbital calculations. A multicenter integral is decomposed into the sum of single‐center integrals using nuclear weight functions and calculated using Gaussian quadrature rules. The decomposed single‐center integrands show strong anisotropy. With a careful selection of the Gaussian quadrature rule according to the anisotropy, it is possible to obtain an accuracy of 13 digits with a small number of integration points for the overlap integrals, normalization integrals, and molecular integrals for the hydrogen molecule. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 509–523, 1999