Hydrogen bonds molecular modeling

Key words Lecithin - phosphatidyl-ethanolamine - self-organization -reverse micelles - polymer-like micelles - organogel - hydrogen bonds - molecular model... 

In solution, although solute contributions can generally be singled out, difficulties arise sometimes solvent-solute interactions may induce a shift of the solute absorption and consequently of its susceptibility or hydrogen bonded molecular complexes may modify the liquid structure. This situation has been studied both theoretically and experimentally by Zyss and Berthier (10) and by Ledoux and Zyss (13) in the case of urea derivatives in various solvents and in crystal showing the importance of environment considerations and thus the limitations of an oriented gas model for crystals. 

The LSER approach relates a bulk property, P, to molecular parameters thought to account for cavity formation, dipole moment/polarizability, and hydrogen-bonding effects at the molecular level. The cavity term models the energy needed to provide a solute molecule-sized cavity in the solvent. The dipole moment/polarizability terms model dipole and induced dipole interactions between solute and solvent these can be viewed as related to dispersion interactions. The hydrogen-bonding terms model HBA basicity and EIBD acidity interactions. 

Ken Jordan received his Ph.D. in physical chemistry in 1974 under the direction of Bob Silbey at MIT. He then joined the Department of Engineering and Applied Science, Yale University, as a J.W. Gibbs Instructor, being promoted to Assistant Professor in 1976. In 1978 Professor Jordan moved to the Chemistry Department at the University of Pittsburgh where he is now Professor and Director of the Center for Molecular and Materials Simulations. His interest in the application of computers to chemical problems stems from his graduate student days. Professor Jordan s recent research has focused on the properties of hydrogen-bonded clusters, modeling chemical reactions on surfaces, electron-induced chemistry and the development of new methods for Monte Carlo simulations. 

CoMSIA (in Ref. [25]—CoMSIA2) models are based on electrostatic and steric fields molecular fields and also involve contributions from the hydrophobic and two hydrogen-bonding molecular fields. All CMF models are based on the use of all afore-mentioned five types of molecular fields. All CoMFA and CoMSIA models were obtained by using a lattice with 2 A spacing expanding at least 4 A in each direction beyond aligned molecules. Only the most predictive CoMFA and CoMSIA models are included in the Table 13.3. 

The system belongs to the normal type of hydrogen bonded molecular complexes forming a SM potential in the gas phase. In water, NH -HF is most stable as ionic complex NH +f7 However, most of the calculations using different levels of quantiim theory as well as different kinds of solvation models find a SM potential representing a molecular complex. An exception forms the application of the... 

The interaction model described above has been extensively tested and successfully used in many calculations on weak van der Waals as well as hydrogen bonded molecular clusters (see Hydrogen Bonding I and Hydrogen Bonding 2). It also forms the kernel of many solute/solvent potentials that are used in the various approaches to the modeling of solvation. 

Hydrogen-bonded clusters are an important class of molecular clusters, among which small water clusters have received a considerable amount of attention [148, 149]. Solvated cluster ions have also been produced and studied [150, 151]. These solvated clusters provide ideal model systems to obtain microscopic infonnation about solvation effect and its influence on chemical reactions. 

Figure C3.2.7. A series of electron transfer model compounds with the donor and acceptor moieties linked by (from top to bottom) (a) a hydrogen bond bridge (b) all sigma-bond bridge (c) partially unsaturated bridge. Studies with these compounds showed that hydrogen bonds can provide efficient donor-acceptor interactions. From Piotrowiak P 1999 Photoinduced electron transfer in molecular systems recent developments Chem. Soc. Rev. 28 143-50.

Many phenomena ask for local, site-specific properties of a molecule such as the partial charge on a specific atom in a molecule or the hydrogen bond donor ability of a certain OH group. It would be highly desirable to have methods as simple as an additivity model to estimate such site-specific molecular properties. 

The stereoselectivity of this reaction depends on how the alkene approaches the catalyst surface As the molecular model m Figure 6 3 shows one of the methyl groups on the bridge carbon lies directly over the double bond and blocks that face from easy access to the catalyst The bottom face of the double bond is more exposed and both hydrogens are transferred from the catalyst surface to that face... 

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