Embedding molecule

Once the electron density of the embedded molecule is evaluated by the SCRF calculations, the free-energy component which is due to the solvent polarization and can be expressed as ... 

MicroEnv represents the interactions between the molecules of the environment and the embedded molecule(s) ... 

Ay and EC are constants which do not depend on the geometry of neither the embedded molecule nor the atoms from the environment ... 

The first term in Eq. 4.26 represents Van der Waals forces between atoms of the microscopic environment and the embedded molecule, this term is not involved in the construction of the Fock matrix. The second one represents Coulomb interactions between the embedded electron density and the electric charge distribution in the environment which is approximated by point charges. 

Molecular junctions represent model configurations, in which a voltage bias, as imposed by an outside source, triggers an electric current between two electrodes and a single embedded molecule, which reflects the electronic characteristics of the molecular junctions (Fig. 1). 

Calculation of nuclear magnetic shielding tensors for embedded molecules... 

In the popular fluid mosaic model for biomembranes, membrane proteins and other membrane-embedded molecules are in a two-dimensional fluid formed by the phospholipids. Such a fluid state allows free motion of constituents within the membrane bilayer and is extremely important for membrane function. The term "membrane fluidity" is a general concept, which refers to the ease of motion for molecules in the highly anisotropic membrane environment. We give a brief description of physical parameters associated with membrane fluidity, such as rotational and translational diffusion rates, order parameters etc., and review physical methods used for their determination. We also show limitations of the fluid mosaic model and discuss recent developments in membrane science that pertain to fluidity, such as evidence for compartmentalization of the biomembrane by the cell cytoskeleton. 

Water is so familiar a liquid that we do not always realize that a number of casual looking chemical properties it displays are indeed exceptional. Liquid water is thus unique to ionize acids and bases, to dissolve such ions as HjO, OH , or other cations and anions. It is also an exceptional solvent for organic molecules, and in some cases, the asymmetric solubility of amphiphile molecules is at the origin of well-defined structural entities, which play important roles in both chemical and biomedia. As for any other liquid, the fluidity of liquid water allows it to have molecules different from H2O embedded in it. The presence of a hyper-dense H-bond network furthermore provides liquid water with possibilities to accommodate embedded molecules other than H2O, D2O or HDO. Other liqnids are far to display these possibilities to the same extent. We examine these different points snccessively. 

To generalize the procedures of Sections 5.2 and 5.3.1 to the liquid phase, one can start from the full microscopic description of the system. The Hamiltonian for the whole system is partitioned into a gas-phase component, as given in Eq. (1), for a reactive embedded molecule or embedded cluster (note an embedded cluster is often called a supermolecule) in the absence of the solvent, and a solvent component that includes coupling between the solvent and reactive subsystem ... 

Relativistic and electron correlation effects play an important role in the electronic structure of molecules containing heavy elements (main group elements, transition metals, lanthanide and actinide complexes). It is therefore mandatory to account for them in quantum mechanical methods used in theoretical chemistry, when investigating for instance the properties of heavy atoms and molecules in their excited electronic states. In this chapter we introduce the present state-of-the-art ab initio spin-orbit configuration interaction methods for relativistic electronic structure calculations. These include the various types of relativistic effective core potentials in the scalar relativistic approximation, and several methods to treat electron correlation effects and spin-orbit coupling. We discuss a selection of recent applications on the spectroscopy of gas-phase molecules and on embedded molecules in a crystal enviromnent to outline the degree of maturity of quantum chemistry methods. This also illustrates the necessity for a strong interplay between theory and experiment. 

In this work, an alternative strategy for deriving the spin-density of an embedded molecule is used. Instead of applying Kohn-Sham theory to the whole system, the spin/electron densities of different subsystems are treated separately. The two subsystems correspond to a) the embedded molecule the radical b) the embedding molecule(s) the atoms or molecules forming the complex with the radical. For a given electron-density of the embedding molecules. 

Finally, it is important to note that all the components of the KSCED effective potential arising from the interaction with the embedding molecule(s) are represented using only explicit functions of the electron densities of differ-... 

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