Is molecular rotation really influenced by subtle changes in molecular shape?

In an attempt to seek out whether the reorientation time of a solute molecule is influenced by marginal changes to its shape, rotational relaxation of four coumarin solutes that are almost identical in size but subtly distinct in shape has been investigated in a viscous nonpolar solvent as a function of temperature. It has been observed that the reorientation times of the four coumarins differ significantly from one another. The four solutes have been treated as asymmetric ellipsoids and Stokes-Einstein-Debye hydrodynamic theory has been employed to calculate the shape factors and boundary condition parameters. The measured reorientation times when normalized by respective shape factors and boundary condition parameters can be scaled on a common curve, which is an indication that ellipsoid based hydrodynamic theory is adequate to model the reorientation times even when the differences in the shapes of the solute molecules are minimal.     

An improved molecular connectivity index

Through modification of the delta values of the molecular connectivity indexes, and connecting the quantum chemistry with topology method effectively, the molecular connectivity indexes are converted into quantum-topology indexes. The modified indexes not only keep all information obtained from the original molecular connectivity method but also have their own virtue in application, and at the same time make up some disadvantages of the quantum and molecular connectivity methods.     

Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, first principles MD or Car-Parrinello method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics/chemistry (liquid phosphorus). Dynamical, finite temperature, simulations deriving interatomic forces from state-of-the-art density functional calculations represent a substantial advance over both (i) traditional pointwise total energy and electronic band structure calculations and (ii) classical MD simulations with empirical or semi-empirical forces, and have already yielded qualitatively new insights in several fields.     

Fractal phenomena in molecular mechanics calculation

It is proposed that in molecular mechanics calculation points belonging to various stable or meta-sta-ble conformtrs are mixed up and form fractal structures in conformation space.The calculation results show the following two phenomena:(i)Two levels of structure with fractal feature were observed.Around the conformer without mirror symmetry points belonging to the conformer and its enantiomer are mixed up and form the first level of fractal structure; on the boundary of the attractive basin o{ each atlractor,points belonging to different attractors form the second level of fractal structure.(ii) The variation of molecular mechanics parameters will influence the structure and area of each attractive basin significantly The above phenomena may become the basis of a new method for solving the troublesome multi-minimum-point problem in molecular mechanics calculation.     

Nanoscale segregation,molecular recognition and fluorophobic effect – from molecular design towards complex mesophase morphologies

Mesomorphic structure formation of hydrogen-bonded complexes of amino substituted 1,3,5-triazines with complementary (semiperfluoro)alkoxybenzoic acids is presented. The substitution pattern of both components was modified systematically in order to elucidate the influence of molecular parameters on the mesophase morphologies of the binary mixed systems. The phase sequence of the triazines, and of their associates with the acids, spans the range from smectic layer structures to discontinuous cubic phases composed of closed inverted micelles. Columnar phases with various two-dimensional lattice symmetries and bicontinuous cubic phases were found as intermediates. The mesophase morphologies are discussed in terms of the microsegregation of rigid polar, lipophilic and fluorinated molecular blocks in different sub-spaces along with tailoring the shape of (curved) aggregates by the space requirement of incompatible molecular fragments.     

Steered molecular dynamics simulations of protein-ligand interactions

Molecular recognition and specific protein-ligandinteractions are central to many biochemical processes,such as enzyme catalysis, assembly of organelles, en-ergy transduction, signaling, diverse control functions,and replication, expression and storage of the geneticmaterial[1]. Moreover, protein-ligand interactions pro-vide the mechanism of many drug therapies and un-derstanding of such interactions is thus significant forrational drug design[1,2]. For the experimental studiesof protein-ligan…