Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Tailoring approach for exploring electron densities and electrostatic potentials of molecular crystals

Experimental and theoretical studies of electron densities and the corresponding derived entities such as electrostatic potentials have been the primary means of understanding the chemical nature and electronic properties of crystalline substances. Conventional crystal calculation methods such as the embedded cluster models are capable of performing calculations on small and medium-sized molecules, while periodic ab initio methods can treat crystals with up to 200 atoms per unit cell. A linear scaling method, viz. the molecular tailoring approach, has recently been developed for obtaining ab initio quality one-electron properties. In the present study, the molecular tailoring approach is employed to generate electron density, electrostatic potential and interaction density maps with the ibuprofen crystal as a test case. The interaction density and electrostatic potential maps produced in the present work succinctly bring out the actual crystalline environment around a given reference molecule by including the interactions with atoms in its neighborhood. The results obtained from the molecular tailoring approach may thus be expected to enhance our understanding of the environment in the crystalline material with reasonably small computational effort.Contribution to the Jacopo Tomasi Honorary Issue     

Growth of ramification-like ZnO rods in the presence of polyaniline

To obtain new materials with synergetic or complementary behaviors, polyaniline composite filled with ZnO rods in ramification-like structure was prepared by a hydrothermal approach. Comparative experiments of ZnO preparation in the presence of some metal ions were also carried out. The results indicated that the morphology of ZnO was strongly affected by the preparation condition. The method to grow ZnO rods in the presence of polyaniline offers a simple approach to obtain polyaniline composite filled with linear ZnO structure. The results of X-ray photoelectron spectroscopy show that the strong interaction between ZnO and polyaniline possibly exists to cause the charge transfer.     

Nonlinear Optical Properties of Tri—nuclear Transition Metal Clusters M—（μ—S）s—M′（M=Mo,W;M′=Cu,Ag,Au）

The static polarizabilities and the second-order hyperpolarizabilities of a series of tri-nuclear metal cluster models MS4(M′PPh3)2(M′PPh3)(M=Mo,W;M′=Cu,Ag,Au)have been calculated within the first-principle theoretical framework. The model clusters have two fragments of rhombic units and it is the charge ransfer from one of these moieties to the other that is responsible for nonlinear optical property. This kind of electronic delocaization, differentiated from that of planar π-system, is very interesting and is worthy for further investigation.     

Development of an Amperometric Sensor Highly Selective For Dopamine and Analogous Compounds Determination Using Bis(2,2′‐Bipyridil) Copper(II) Chloride Complex

The use of [Cu(bipy)₂]Cl₂?6H₂O as a biomimetic catalyst in the construction of an amperometric sensor for dopamine determination is reported. The sensor was prepared modifying a glassy carbon electrode with a Nafion membrane doped with [Cu(bipy)₂]Cl₂?6H₂O complex. The sensor presented a higher response in 0.25 mol L^?1 phosphate buffer solution (pH 7.0), with an applied potential of ?50 mV (vs. SCE). In the optimized operational conditions, a linear response range between 35 and 240 μmol L^?1, with a sensitivity of 2.02±0.07 nA l μmoL^?1 cm^?2 and detection limit of 8.0 μmol L^?1 were typically observed for the sensor. The response time presented for this sensor was 0.5 s, presenting the same response for at least 40 successive measurements, with good repeatability (3.0%) expressed as relative standard deviation for n=6. The difference of the response between four sensor preparations was 4%. A detailed investigation about the sensor response for other sixteen phenolic compounds and interfering species were carried out. The sensor was applied in the determination of dopamine in pharmaceutical preparation with success.     

Semi‐classical formulation of time‐dependent discrete variable representation method

In this article, we apply a novel time‐dependent discrete variable representation (TDDVR) method proposed by Barkakaty and Adhikari to investigate tunneling through an Eckart barrier. This semi‐classical method is theoretically rigorous and straightforward to implement. Among the TDDVR formulations, this report presents the first derivation of a rigorous form of quantum force (QF) for the present perspective. The validity of this semi‐classical approach is demanded based on the excellent agreement of the tunneling probability with the corresponding quantum results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Convergence of an augmented Lagrange algorithm for nonlinear optimizations with second-order cone constraints

An augmented Lagrange algorithm for nonlinear optimizations with second-order cone constraints is proposed based on a Löwner operator associated with a potential function for the optimization problems with inequality constraints. The favorable properties of both the Löwner operator and the corresponding augmented Lagrangian are discussed. And under some mild assumptions, the rate of convergence of the augmented Lagrange algorithm is studied in detail.     

Exponential stability of discrete-time systems with slowly time-varying delays

Slowly time-varying delays are seldom, but do need to be, considered in the context of discrete-time systems. This paper addresses the exponential stability issue of discrete-time systems with slowly time-varying delays. The basic idea is to transform, by utilizing the switching transformation approach, the original system with slowly time-varying delays into an equivalent switched system with special switching signal. Different types of delays correspond to different types of switching signals, and the stability issue of the original system is converted into that of a switched system. It is the first time that the method of switched homogeneous polynomial Lyapunov function is applied to general delayed systems. Some sufficient exponential stability conditions for the original system are proposed in several situations. It is numerically shown that the conservativeness of the proposed conditions reduces as the degree of the switched homogeneous polynomial Lyapunov function increases.     

Retrieval and chaos in extremely dilutedQ-Ising neural networks

Using a probabilistic approach, the deterministic and the stochastic parallel dynamics of aQ-Ising neural network are studied at finiteQ and in the limitQ. Exact evolution equations are presented for the first time-step. These formulas constitute recursion relations for the parallel dynamics of the extremely diluted asymmetric versions of these networks. An explicit analysis of the retrieval properties is carried out in terms of the gain parameter, the loading capacity, and the temperature. The results for theQ network are compared with those for theQ=3 andQ=4 models. Possible chaotic microscopic behavior is studied using the time evolution of the distance between two network configurations. For arbitrary finiteQ the retrieval regime is always chaotic. In the limitQ the network exhibits a dynamical transition toward chaos.     

烯丙基硅烷的一步法合成研究

采用一步合成方式,将3-溴丙烯与金属镁在以甲苯和供电子溶剂(乙醚或THF)构成的混合溶剂中进行反应,继而与四氯化硅反应,成功合成了四烯丙基硅烷,其产率在乙醚与3-溴丙烯的摩尔比为4(V甲苯/V乙醚=1·1)时达到极值,超过了91%。研究同时发现,选择THF代替乙醚时,同样在THF与3-溴丙烯的摩尔比为4(V甲苯/VTHF=1·7)时产率达到极值(63·12%)。本过程可提高产率,降低成本,是一条好的生产四烯丙基硅烷的路线。