Molecular systems numerical study

Chitosan-based nano- and microparticles are widely used for fabrication of controlled dmg release systems. Numerous studies have demonstrated that chitosan and its derivatives (A-trimethyl chitosan, mono-A-carboxymethyl chitosan, etc.) are effective and safe for absorption enhance to improve mucosal (nasal, peroral) delivery of hydrophylic macromolecules, such as peptide and protein dmgs as well as heparins [37,38]. This absorption enhancing effect of chitosan is caused by the opening of intercellular tight junctions, thereby favoring the paracellular transport of macro-molecular dmgs. Recently, a series of successful model chitosan-based polymer systems for mucosal dmg delivery have been reported. Thus, Lim et al. [39] have proposed novel polymer microparticles based on combination of hyaluronic acid and chitosan hydroglutamate... 

A major advance in force measurement was the development by Tabor, Win-terton and Israelachvili of a surface force apparatus (SFA) involving crossed cylinders coated with molecularly smooth cleaved mica sheets [11, 28]. A current version of an apparatus is shown in Fig. VI-4 from Ref. 29. The separation between surfaces is measured interferometrically to a precision of 0.1 nm the surfaces are driven together with piezoelectric transducers. The combination of a stiff double-cantilever spring with one of a number of measuring leaf springs provides force resolution down to 10 dyn (10 N). Since its development, several groups have used the SFA to measure the retarded and unretarded dispersion forces, electrostatic repulsions in a variety of electrolytes, structural and solvation forces (see below), and numerous studies of polymeric and biological systems. 

When studying molecular systems one encounters two almost insurmountable difficulties (1) That of numerically treating the non-adiabatic coupling terms that are not only spiky—a feature that is in itself a recipe for numerical... 

Kamlet-Taft Linear Solvation Energy Relationships. Most recent works on LSERs are based on a powerfiil predictive model, known as the Kamlet-Taft model (257), which has provided a framework for numerous studies into specific molecular thermodynamic properties of solvent—solute systems. This model is based on an equation having three conceptually expHcit terms (258). 

Solving Newton s equation of motion requires a numerical procedure for integrating the differential equation. A standard method for solving ordinary differential equations, such as Newton s equation of motion, is the finite-difference approach. In this approach, the molecular coordinates and velocities at a time it + Ait are obtained (to a sufficient degree of accuracy) from the molecular coordinates and velocities at an earlier time t. The equations are solved on a step-by-step basis. The choice of time interval Ait depends on the properties of the molecular system simulated, and Ait must be significantly smaller than the characteristic time of the motion studied (Section V.B). 

The static dipole polarizability is the linear response of an atomic or molecular system to the application of a weak static electric field [1], It relates to a great variety of physical properties and phenomena [2-5]. Because of its importance, there have been numerous ab initio calculations of isolated atomic and molecular polarizabilities [6-14]. Particular theoretical attention has been dedicated to the polarizability of free atomic anions [15-21] because of its fragility and difficulty in obtaining direct experimental results. In recent years theoretical studies have... 

The possibility to carry out conformational studies of peptides at low concentrations and in the presence of complex biological systems represents a major advantage of fluorescence spectroscopy over other techniques. Fluorescence quantum yield or lifetime determinations, anisotropy measurements and singlet-singlet resonance energy transfer experiments can be used to study the interaction of peptides with lipid micelles, membranes, proteins, or receptors. These fluorescence techniques can be used to determine binding parameters and to elucidate conformational aspects of the interaction of the peptide with a particular macro-molecular system. The limited scope of this chapter does not permit a comprehensive review of the numerous studies of this kind that have been carried and only a few general aspects are briefly discussed here. Fluorescence studies of peptide interactions with macromolecular systems published prior to 1984 have been reviewed. 

The variational principle has not been widely used in diffusion kinetic problems. Nevertheless, it is such a powerful technique that it is suitable for discussing the many-body problems which have still to be tackled. Wherever approximate methods are necessary, the variational principle should be considered. The trial function(s) should be chosen with care, based on a good idea of the nature of the trial function from its behaviour in certain asymptotic limits. The only application known to the author of the variation principle to a numerical study of a diffusion kinetic problem on a molecular system is that of Delair et al. [377]. They used the variational principle to generate an implicit finite difference scheme for solving the Debye—Smoluchowski equation. Interesting comments have been made by Brykalski and Krason more in the context of heat diffusion [510]. 

To understand the fundamental photochemical processes in biologically relevant molecular systems, prototype molecules like phenol or indole - the chromophores of the amino acids tyrosine respective trypthophan - embedded in clusters of ammonia or water molecules are an important object of research. Numerous studies have been performed concerning the dynamics of photoinduced processes in phenol-ammonia or phenol-water clusters (see e. g. [1,2]). As a main result a hydrogen transfer reaction has been clearly indicated in phenol(NH3)n clusters [2], whereas for phenol(H20)n complexes no signature for such a reaction has been found. According to a general theoretical model [3] a similar behavior is expected for the indole molecule surrounded by ammonia or water clusters. As the primary step an internal conversion from the initially excited nn state to a dark 7ta state is predicted which may be followed by the H-transfer process on the 7ia potential energy surface. 

In Ref. [4] we have studied an intense chirped pulse excitation of a molecule coupled with a dissipative environment taking into account electronic coherence effects. We considered a two state electronic system with relaxation treated as diffusion on electronic potential energy surfaces with respect to the generalized coordinate a. We solved numerically equations for the density matrix of a molecular system under the action of chirped pulses of carrier frequency a> with temporal variation of phase [Pg.131]

Metalloreceptors, and the supermolecules that they form, thus open up a vast area for the study of interactions and reactions between simultaneously co-bound organic and inorganic species [4.67,4.68]. In view of the number of metal-ion complexes known and of the various potential molecular substrates, numerous types of metalloreceptors may be imagined that would be of interest as abiotic chemical species or as bioinorganic model systems. 

A new and efficient computational strategy has been presented, that simplifies the calculation of the vibrational frequencies of a molecular system adsorbed on moderate to large cluster models. This procedure is based on a certain hypothesis and assumption. Nevertheless, present results show that these do not affect the numerical accuracy of the calculated frequencies. An important consequence of this strategy is that largely simplifies the study of the effect of a uniform electric field on the frequencies of an adsorbed species. This is because it is not necessary to recalculate the normal coordinates at each value of the electric field. The method has been presented in connection to a cluster model representation of the surface, but it can be directly applied to periodical approaches without further modification. 

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