An investigation into the construction of molecular models by the template joining method

Summary The results of a wide-ranging investigation into some of the different methods available for performing the joining of templates to build molecular models show that the choice of algorithm can significantly affect the quality of the results obtained, and different algorithms are most suited to particular categories of join.     

Cavity search: An algorithm for the isolation and display of cavity-like binding regions

Summary A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand.     

Etude DFT du mécanisme des réactions de cycloaddition dipolaire-1,3 de la C,N-diphénylnitrone avec des dipolarophiles fluorés de type éthylénique et acétylénique

Structures and energetics of reactants, transition states and cycloadducts of cycloadditions of nitrone with three-fluorinated dipolarophiles have been investigated with the density functional theory method B3LYP/6-31G^*. Analysis of the results on the different reaction pathways shows that the reaction takes place along a concerted mechanism and proceeds more or less synchronously. The FMO analysis shows a strong HOMO_dipole-LUMO_{dipolarophile} interaction as the principal reason for the reactivity in these 1,3-dipolar cycloaddition reactions. Regioselectivity of the products of the reaction is predicted reliably by our calculations, the results provide a good prediction of the relatives rates observed experimentally as the dipolarophiles are varied.     

Trehalose-based cyclodextrin analogs: cyclotrehalans (CTs)

A new concept for the de novo synthesis of artificial glyconanocavities is presented. The use of alternating α,α′-trehalose building blocks and (thio)urea segments allows the efficient synthesis of a new family of cyclooligosaccharides, namely cyclotrehalans (CTs), featuring a convex-shaped cavity with an apolar environment. CTs are designed to exhibit molecular inclusion abilities similar to that of cyclodextrins (CDs). Contrary to CDs, CTs expose the monosaccharide β-face to the inner cavity, while the (thio)urea tethers provides some conformational adaptability. High-yielding syntheses of a series of CTs and a preliminary evaluation of their inclusion properties are reported.     

The Role of Binary and Many-centre Molecular Interactions in Spin Crossover in the Solid State. Part I. Equation for Free Energy

Summary. A formalism has been developed that describes spin crossover equilibrium in the solid state by taking into account the effects of n nearest neighbours of a given molecule on its partition function. In this way binary and many-body interactions of the order n + 1 are included into the theoretical model and represented by non-ideality parameters connected with the splitting of free energy levels. Binary interactions are characterised by the main splittings whereas higher order interactions manifest themselves in asymmetries of splittings within multiplets. The contribution of molecular interactions can also be written in terms of formal excess free energies of the second, third, fourth and higher orders. Simple relationships between excess free energies and parameters of multiplets have been found for binary, ternary and quaternary interactions. This formalism is reduced to that of the model of binary interactions when effects of surroundings are additive leading to equidistant free energy multiplets. Higher order interactions may cause an abrupt spin crossover but in a limited range of compositions around the transition point. The regression of experimental transition curves of one-step spin crossover may yield estimates of excess energies up to the fifth order.     

Monte Carlo simulation of polarizable systems: Early rejection scheme for improving the performance of adiabatic nuclear and electronic sampling Monte Carlo simulations

An early rejection scheme for trial moves in adiabatic nuclear and electronic sampling Monte Carlo simulation (ANES-MC) of polarizable intermolecular potential models is presented. The proposed algorithm is based on Swendsen–Wang filter functions for prediction of success or failure of trial moves in Monte Carlo simulations. The goal was to reduce the amount of calculations involved in ANES-MC electronic moves, by foreseeing the success of an attempt before making those moves. The new method was employed in Gibbs ensemble Monte Carlo (GEMC) simulations of the polarizable simple point charge-fluctuating charge (SPC-FQ) model of water. The overall improvement in GEMC depends on the number of swap attempts (transfer molecules between phases) in one Monte Carlo cycle. The proposed method allows this number to increase, enhancing the chemical potential equalization. For a system with 300 SPC-FQ water molecules, for example, the fractions of early rejected transfers were about 0.9998 and 0.9994 at 373 and 423 K, respectively. This means that the transfer moves consume only a very small part of the overall computing effort, making GEMC almost equivalent to a simulation in the canonical ensemble.     

Structure formation and dynamics of water in strong external electric fields

We have performed molecular dynamics computer simulations of water in homogeneous external electric fields which were varied in a wide range of field strengths. The dielectric response is found to be linear up to fields E₀≈0.01 V/Å from where dielectric saturation effects become important. At fields of E₀≈3 V/Å a phase transition into an ordered, ice-like structure is observed, which is stabilized through hydrogen-bonds. With an increasing external electric field, the frequency spectrum of the water dynamics shows a remarkable red shift of the intramolecular modes and a blue shift of the librational motions, where the frequency varies quadratically with the field strength. A simple analytical model is discussed which reproduces the observed behavior.     

Molecular potential-energy surfaces for chemical reaction dynamics

This paper reviews the construction of molecular potential-energy surfaces by an interpolation method which has been developed over the last several years. The method uses ab initio quantum chemistry calculations of the molecular electronic energy in an automated procedure to construct global potential- energy surfaces which can be used to simulate chemical reactions with either classical or quantum dynamics. The methodology is explained and several applications are presented to illustrate the approach. Received: 22 February 2002 / Accepted: 2 May 2002 / Published online: 6 November 2002 Correspondence to: M. A. Collins e-mail: collins@rsc.anu.edu.au Acknowledgements. The methods described in this overview are the result of collaborations with former members of my group, in particular with Josef Ischtwan, Meredith Jordon, Keiran Thompson and Ryan Bettens. I am also indebted for inspiration gained from many discussions with my colleagues Leo Radom and Donghui Zhang (National University of Singapore). This work has been supported by the Supercomputer Facility of the Australian National University and the Australian Partnership for Advanced Computing.     

Synthesis of a novel rigid molecule family for the investigation of electron and energy transfer

Three new rigid bridging ligands for metal complexation (7=bmb, 8=bqb and 11=btb) were prepared from a rigid triptycene spacer connected to two bipyridine ligands using a Horner–Emmons type reaction. The triptycene spacer is substituted by methoxy groups in the case of bmb and in the case of bqb by a benzoquinone substituent. The corresponding metal complexes (ruthenium and/or osmium) were synthesised and the different luminescence behaviour was tested. They show great potential for the investigation of intramolecular electron and energy transfer reactions. The dinuclear metal complex Ru---bqb---Os is an interesting system in which the bridging ligand bqb acts as a redox switch, able to tune the conductivity for energy or electrons across the bridge.     

聚合物体系散射函数的热力学基础

利用链段浓度和链头浓度的概念，根据热力学涨落理论，给出了聚合物二元共混体系ｄｅＧｅｎｎｅｓ散射函数的一个普遍的热力学证明，指出了这个函数和Ｆｌｏｒｙ－Ｈｕｇｇｉｎｓ共混自由能公式一样，也依赖于忽略构象涨落的假设．