An approach to channel type molecular structures. 1. Synthesis ofBouquet-shaped molecules based on an [18]-O6 polyether macrocycle

An approach to a transmembrane cation channel is described. It is based on the grafting of oxygen bearing side-chains on a macrocyclic polyether unit that constitutes the organizing core. The resulting species has a structure of overall bouquet shape. The synthesis of such a molecule . _M ⁰ ,14a is described, together with that of its analogue bearing polymethylene side-chains _M ^C ,14b. The physicochemical properties of these molecules indicate that they possess the features expected on the basis of their structure.This paper is dedicated to the memory of the late Dr C. J. Pedersen.     

Molecular weight distribution in emulsion polymerization. I. The homopolymer case

A model for evaluating the instantaneous degree of polymerization distribution of homopolymers produced in emulsion, based on the mathematics of the Markov chains, is developed. The model accounts for any number of active chains per particle, as well as for the two fundamental mechanisms of chain termination: mono- and bi-molecular, both by combination and by disproportionation. The core of the model is the so called subprocessmain process treatment, which allows us to correctly evaluate the degree of polymerization of the chains growing in the polymer particles, by distinguishing between the events experienced by the polymer chain which imply a change of its degree of polymerization (subject transitions) and those which imply only a change in the particle state (environment transitions). This is obtained by properly defining the one-step transition probability matrix of the relevant Markov process. Once this is done, the evaluation of the distribution of the degrees of polymerization reduces to a few simple operations among matrices. Explicit expressions for the instantaneous probability density functions and the relative cumulative distributions are obtained. The application of such relationships is facilitated by the numerical procedures reported in the Appendices. The results of the model developed in this work are in agreement with those of earlier models in the range of parameter values of practical interest. In the limit of very low molecular weights, only the model developed in this work provides the correct answer. Moreover, a much more significant result is its applicability to the case of emulsion copolymerization, as it is shown in Part II.     

Pattern recognition strategies for molecular surfaces. II. Surface complementarity

Fuzzy logic based algorithms for the quantitative treatment of complementarity of molecular surfaces are presented. Therein, the overlapping surface patches defined in article I1 of this series are used. The identification of complementary surface patches can be considered as a first step for the solution of molecular docking problems. Standard technologies can then be used for further optimization of the resulting complex structures. The algorithms are applied to 33 biomolecular complexes. After the optimization with a downhill simplex method, for all these complexes one structure was found, which is in very good agreement with the experimental results.     

A Central Partition of Molecular Conformational Space. III. Combinatorial Determination of the Volume Spanned by a Molecular System

In the first work of this series (Gabarro-Arpa, Comp. Biol. Chem. 27 (2003) 153–159) it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the space into a hierarchical set of cells that can be encoded by the face lattice poset of the arrangement. The model however, lacked explicit rotational symmetry, which made impossible to distinguish rotated structures in conformational space. This problem was solved in a second work (Gabarro-Arpa, Proc. 26th Ann. Int. Conf. of the IEEE EMBS (San Franciso, 2004) 3007–3010) by sorting the elementary 3-dimensional components of the molecular system into a set of morphological classes that can be properly oriented in a standard 3-D reference frame. This also made possible to find a solution to the problem that is being addressed in the present work: for a molecular system immersed in a heat bath we want to enumerate the subset of cells in conformational space that are visited by the molecule in its thermal wandering. If each visited cell is a vertex on a graph with edges to the adjacent cells, here it is explained how such graph can be built.     

Temperature-dependent and friction-controlled electrochemically induced shuttling along molecular strings associated with electrodes.

The temperature and solvent composition dependence of the electrochemically stimulated rate of shuttling of the redox-active cyclophane, cyclobis(paraquat-p-phenylene), on a molecular string has been studied. The molecular string includes a pi-donor diiminebenzene-site that is associated on one side with an electrode, and stoppered on the other side with an adamantane unit. The cyclophane rests on the pi-donor site, owing to stabilizing pi-donor-acceptor interactions. Electrochemical reduction of the cyclophane units, to the bis-radical cation cyclophane, results in the shuttling of the reduced cyclophane towards the electrode, a process that is driven by the removal of the stabilizing donor-acceptor interactions, and the electrostatic attraction of the reduced product by the electrode. The latter process is energetically downhill, and is temperature-independent. Upon oxidation of the reduced cyclophane that is associated with the electrode, the energetically uphill shuttling of the oxidized cyclophane to the pi-donor site proceeds. The rate of this translocation process has been found to be temperature-dependent, and controlled by the solvent composition. The experimental results have been theoretically analyzed in terms of Kramers' molecular friction model. The theoretical fitting of the experimental results, using solutions of variable composition, reveals that the rate-constants for the uphill reaction in a pure aqueous solution follow the temperature-dependence of the viscosity of water. The results demonstrate the significance of friction phenomena in shuttling processes within molecular machines.