Example calculations molecular characteristics

Empirical, semiempirical, and ab initio methods have been used extensively to calculate molecular descriptors. These molecular property descriptors help capture important characteristics of compounds such as bioavailability and receptor affinity. Descriptors such as octanol-water partition coefficient (log P), HOMO/LUMO energies, hammett a, total energy, heats of formation, ionization potential, atomic charges, electron densities, dipole/quadrupole moments, volume, and polar surface area are common examples. For an excellent review of physicochemical descriptors, the reader is directed to the following reference. ... 

We now consider a more realistic case. Let the saturated density of pure smectitic clay (for example, beidellite) be about 1.8[Mg/m ]. The crystal density of the beidellite determined from an MD simulation is found to be 2.901 [Mg/m ]. A stack is assumed to consist of nine minerals. The molecular formula of the hydrated beidellite is Nai/3Al2[Sin/3Ali/3]Oio(OH)2 nH20 where n is the number of water molecules in an interlayer space. We assume that n = 1, 3, 5, and the distance between two minerals (i.e., the interlayer distance) can be obtained from Fig. 8.4 from this, we can determine the volume of external water that exists on the outside of the stack. For each case of n = 1, 3, 5 we calculate the characteristic functions as shown in Fig. 8.10 (note that the scale is different in each case). Then we compute the C-permeability as shown in Fig. 8.11. Based on numerous experimental results, Pusch (1994) obtained the permeability characteristics of clays as a function of density as shown in Fig. 8.12. We recall that the permeability of the saturated smectitic clay is not only a function of the density but also of the ratio of interlayer water to the external water, which indicates that there exists a distribution of permeability for the same density. The range of permeability given in Fig. 8.12 with a saturated density of 1.8Mg/m corresponds well to our calculated results, which were obtained using the MD/HA procedure. 

Recently, Hargittai (2009a,b) described the structural characteristics of metal halides, including nonrigid "floppy" molecules, and analyzed the influence of these features on the experimental and calculated molecular parameters. However, the above examples show that the molecular constants provided in the calculation of the thermodynamic functions in the harmonic approximation led to sufficient accurate results for their subsequent use in practical modeling of the thermodynamic equilibria (Chervoimyi and Chervonnaya, 2004g). 

The methods used to describe the electronic structure of actinide compounds must, therefore, be relativistic and must also have the capability to describe complex electronic structures. Such methods will be described in the next section. The main characteristic of successful quantum calculations for such systems is the use of multiconfigurational wave functions that include relativistic effects. These methods have been applied for a large number of molecular systems containing transition metals or actinides, and we shall give several examples from recent studies of such systems. 

For molecular sizes that are amenable by NMR techniques, nucleic acids usually lack a tertiary fold. This fact, together with the characteristic low proton density, complicates NMR structural analysis of nucleic acids. As a result, local geometries and overall shapes of nucleic acids, whose structures have been determined by NMR, usually are poorly defined. Dipolar couplings provide the necessary long-range information to improve the quality of nucleic acid structures substantially [72]. Some examples can be found already in the literature where the successful application of dipolar couplings into structure calculation and structure refinement of DNA and RNA are reported [73-77]. 

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