Flexibility, conformational/molecular

Here the vector rj represents the centre of mass position, and D is usually averaged over several time origins to to improve statistics. Values for D can be resolved parallel and perpendicular to the director to give two components (D//, Dj ), and actual values are summarised for a range of studies in Table 3 of [45]. Most studies have found diffusion coefficients in the 10 m s range with the ratio D///Dj between 1.59 and 3.73 for calamitic liquid crystals. Yakovenko and co-workers have carried out a detailed study of the reorientational motion in the molecule PCH5 [101]. Their results show that conformational molecular flexibility plays an important role in the dynamics of the molecule. They also show that cage models can be used to fit the reorientational correlation functions of the molecule. 

Finally, it is worth while to consider the applicability of these relaxation methods to molecules having flexible conformations. Examples given in the previous Section demonstrated that relaxation rates are able to define either the most probable conformation of a flexible molecular segment, or to specify a range of allowed conformations from the total number of confor-... 

The isolation of crystalline products having mixed polymorphic compositions (often referred to as concomitant polymorphism) remains a topic of interest, even though the phase rule predicts that a system at equilibrium consisting two components (solvent + solute) and three phases (solution + Form I + Form II) is uni variant. Hence, for crystallizations performed at a fixed pressure (typically atmospheric) the system becomes nonvariant and genuine equilibrium can exist at only one temperature. Therefore, concomitant products must be obtained under nonequilibrium conditions. Flexibility in molecular conformation was attributed to the concomitant polymorphs of a spirobicyclic dione [34] and of 3-acetylcoumarin [35],... 

Virtual screening applications based on superposition or docking usually contain difficult-to-solve optimization problems with a mixed combinatorial and numerical flavor. The combinatorial aspect results from discrete models of conformational flexibility and molecular interactions. The numerical aspect results from describing the relative orientation of two objects, either two superimposed molecules or a ligand with respect to a protein in docking calculations. Problems of this kind are in most cases hard to solve optimally with reasonable compute resources. Sometimes, the combinatorial and the numerical part of such a problem can be separated and independently solved. For example, several virtual screening tools enumerate the conformational space of a molecule in order to address a major combinatorial part of the problem independently (see for example [199]). Alternatively, heuristic search techniques are used to tackle the problem as a whole. Some of them will be covered in this section. 

In addition, the results of absorption studies for a series of (i-adrenoceptor blockers in vitro using Caco-2 monolayers and rat intestinal segments have been used to test new descriptors [55]. For this purpose, the authors calculated dynamic molecular surface properties considering all low-energy conformations. Molecular mechanics were used to consider the flexibility of the molecules, and the van der Waals volume (vdW) and water-accessible surface areas were also calculated (Table 4.18 and 4.19). When the dynamic polar vdW surface areas were used in regression analysis to describe cell permeability data obtained in Caco-2 cells and in rat ileum, excellent correlations were obtained (r2 = 0.99 and 0.92 respectively). 

The structure determination of biopolymers using NMR spectroscopy usually involves interactions of protons[216,33. Typically, interactions of protons (nuclear Overhauser effect, NOE) that are close in space but separated by several subunits of the biopolymer are used to establish the folding of the backbone. Distance restraints are then used to compute a structure which is checked by back-calculation of the NOE spectra and comparison with experimental results 361. For large and highly flexible systems molecular dynamics is invaluable for scanning the conformational space. 

Higher + Electronic + Interaction with the environment Spatio-temporal structure (flexibility, conformation) Electronic properties (electron distribution, polarizability, ionisation) Solvation, hydration, partitioning, intermolecular interactions Conformational energy diagrams, computer display Molecular orbitals, electrostatic potential maps Computer display... 

The dendritic core adopts an extended conformation which is possible due to the great flexibility (conformational freedom) of the PAMAM and PPI skeletons. In this way, the molecular model of thick disks proposed for the LC dendrimers with two-terminal chain mesogenic units is transformed into a model consisting of a long cylinder, which is the result of the axial elonga-... 

Problems involving the flexible conformations of cw-decalin are more easily solved with the following chair-chair conformations. The descriptors a and (3 denote that the substituent is below the molecular plane or above the molecular plane, irrespective of axial versus equatorial. 

After asserting the nanostructured nature of ionic liquids, the structural analysis of these fluids continued in two different directions. The first was to check how the built-in flexibility of the isolated ions of the model affect (or are affected by) the nanostructured nature of the ionic liquid, and how that can influence properties like viscosity, electrical conductivity, or diffusion coefficients. It must be stressed that the charges in the CLAP model are fixed to the atomic positions, which means that the most obvious way to probe the relation between the structure of the ionic liquid as a whole in terms of the structure of its individual ions is to investigate the flexibility (conformational landscape) of the latter. The second alternative direction was to probe the structure of ionic liquids not by regarding into the structure of the component ions but by instead using an external probe (for example, a neutral molecular species), solubility experiments with selected solute molecules being the most obvious experimental approach. 

The absorption spectmm of the monomer is essentially equal to the sum of absorptions of its components. On the other hand, the fluorescence quantum yield ofthe ap monomer is much higher than that of any ofthe separate components. These results suggest that association ofthe a- and P-subunits to form an ap monomer results in a reduction ofthe flexibility ofthe molecular skeletons of the bilins without altering their environment in any other spectroscopically significant way, as it is well known that a less flexible chromophore conformation inhibits the excited state from following alternative de-excitation pathways such as internal conversion. In the case of a denatured phycobiliprotein, the absorption is sharply decreased in the visible and it is non-fluorescent. 

The adsorption of proteins from aqueous solution to solid surfaces is the result of a combination of hydrophobic, steric, and electrostatic interactions between the protein, solid surface, and solution [ 1-3]. Numerous studies have been conducted to identify the driving forces governing protein adsorption and dynamics at liquid-solid interfaces and have been reviewed elsewhere [4—8], In the adsorbed state, protein stmcture is likely to be perturbed (Figure 15.1). The unfolded or partially unfolded protein can then adopt various flexible conformations depending on the natures of the solid surface the protein [1, 4, 9-13]. While this has been exploited for various applications [12], uncontrolled adsorption can cause protein degradation, compromised function, and even life-threatening immunogenic responses. The molecular mechanisms of protein adsorption have not been fully elucidated and remain a current area of research [ 10]. 

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