Computational study on the addition of HCN to methanimine catalyzed by formamidine and formamide

In this paper, we have carried out a theoretical study on the addition of HCN to methanimine with formamidine or formamide using second-order Moller-Plesset perturbation (MP2) method with 6-31 + G(d,p) basis sets. At MP2 level. a high-energy, intermediate has been located for each pathway. The addition of HCN to methanimine with formamidine has the lowest free energy barrier according to the calculations at MP2 level. (C) 2004 Elsevier B.V. All rights reserved.

a computational proof of complexity of some restricted counting problems

South Central University

The further understanding of chain topology effect on the properties of single polymer in good solvent: Special behaviors of single tadpole chain

Chain topology strongly affects the static and dynamic properties of polymer melts and polymers in dilute solution. For different chain architectures, such as ring and linear polymers, the molecular size and the diffusion behavior are different. To further understand the chain topology effect on the static and dynamic properties of polymers, we focus on the tadpole polymer which consists of a cyclic chain attached with one or more linear tails. It is found that both the number and the length of linear tails play important roles on the properties of the tadpole polymers in dilute solution. For the tadpole polymers with fixed linear tail length and number, with increasing the degree of polymerization of tadpole polymers, a transition from linear-like to ring-like behavior is observed for both the static and dynamic properties.

Influence of molecular topology on the static and dynamic properties of single polymer chain in solution

The influence of molecular topology on the structural and dynamic properties of polymer chain in solution with ring structure, three-arm branched structure, and linear structure are studied by molecular dynamics simulation. At the same degree of polymerization (N), the ring-shaped chain possesses the smallest size and largest diffusion coefficient. With increasing N, the difference of the radii of gyration between the three types of polymer chains increases, whereas the difference of the diffusion coefficients among them decreases. However, the influence of the molecular topology on the static and the dynamic scaling exponents is small. The static scaling exponents decrease slightly, and the dynamic scaling exponents increase slightly, when the topology of the polymer chain is changed from linear to ring-shaped or three-arm branched architecture. The dynamics of these three types of polymer chain in solution is Zimm-like according to the dynamic scaling exponents and the dynamic structure factors.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Quantitative structure-property relationships for colour reagents and their colour reactions with cerium using computational neural networks

Quantitative structure-activity/property relationships (QSAR/QSPR) studies have been exploited extensively in the designs of drugs and pesticides, but few such studies have been applied to the design of colour reagents. In this work, the topological indices A(x1)-A(x3) suggested in this laboratory were applied to multivariate analysis in structure-property studies. The topological indices of 43 phosphone bisazo derivatives of chromotropic acid were calculated. The structure-property relationships between colour reagents and their colour reactions with cerium were studied using A(x1-Ax3) indices with satisfactory results. The purpose of this work was to establish whether QSAR can be used to predict the contrasts of colour reactions and in the longer term to be a helpful tool in colour reagent design.

Quantitative structure-property relationships for colour reagents and their colour reactions with ytterbium using regression analysis and computational neural networks

In this paper, the new topological indices A(x1)-A(x3) suggested in our laboratory and molecular connectivity indices have been applied to multivariate analysis in structure-property studies. The topological indices of twenty asymmetrical phosphono bisazo derivatives of chromotropic acid have been calculated. The structure-property relationships between colour reagents and their colour reactions with ytterbium have been studied by A(x1)-A(x3) indices and molecular connectivity indices with satisfactory results. Multiple regression analysis and neural networks were employed simultaneously in this study.

STRUCTURE-PROPERTY RELATIONSHIP BETWEEN HALF-WAVE POTENTIALS OF ORGANIC-COMPOUNDS AND THEIR TOPOLOGY

A significant correlation was found between half-wave potentials of organic compounds and their topological indices, A(x1), A(x2), and A(x3). The simplicity of calculation of the index from the connectivity in the molecular skeleton, together with the significant correlation, indicates its practical value. Good results have been obtained by using them to predict the half-wave potentials of some organic compounds.

QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS FOR TOXICITY OF PHENOLS USING REGRESSION-ANALYSIS AND COMPUTATIONAL NEURAL NETWORKS

Quantitative structure-toxicity models were developed that directly link the molecular structures of a et of 50 alkYlated and/or halogenated phenols with their polar narcosis toxicity, expressed as the negative logarithm of the IGC50 (50% growth inhibitor

Impact of difference accuracy on computational properties of vertical grids for a nonhydrostatic model

Starting from nonhydrostatic Boussinesq approximation equations, a general method is introduced to deduce the dispersion relationships. A comparative investigation is performed on inertia-gravity wave with horizontal lengths of 100, 10 and 1 km. These are examined using the second-order central difference scheme and the fourth-order compact difference scheme on vertical grids that are currently available from the perspectives of frequency, horizontal and vertical component of group velocity. These findings are compared to analytical solutions. The obtained results suggest that whether for the second-order central difference scheme or for the fourth-order compact difference scheme, Charny-Phillips and Lorenz ( L) grids are suitable for studying waves at the above-mentioned horizontal scales; the Lorenz time-staggered and Charny-Phillips time staggered (CPTS) grids are applicable only to the horizontal scales of less than 10 km, and N grid ( unstaggered grid) is unsuitable for simulating waves at any horizontal scale. Furthermore, by using fourth-order compact difference scheme with higher difference precision, the errors of frequency and group velocity in horizontal and vertical directions produced on all vertical grids in describing the waves with horizontal lengths of 1, 10 and 100 km cannot inevitably be decreased. So in developing a numerical model, the higher-order finite difference scheme, like fourth-order compact difference scheme, should be avoided as much as possible, typically on L and CPTS grids, since it will not only take many efforts to design program but also make the calculated group velocity in horizontal and vertical directions even worse in accuracy.

Unprecedented 5,5-connected (4(7)center dot 6(3)) (4(8)center dot 6(2)) structural topology: A lead biphosphonate with double layered structure

A new lead(II) phosphonate, Pb[(PO3)(2)C(OH)CH3]center dot H2O (1) was hydrothermally synthesized and characterized by IR, elemental analysis, UV, TGA, SEM, and single crystal X-ray diffraction analysis. X-ray crystallographic study showed that complex 1 has a two-dimensional double layered hybrid structure containing interconnected 4- and 12-membered rings and shows an unusual (5,5)-connected (4(7) . 6(3)) (4(8) .6(2)) topology. (C) 2008 Elsevier B.V. All rights reserved.