Molecular interaction potential

If the atomic or molecular interaction potentials are known, the surface energy for very thin films can be calculated by assuming additivity and integrating over the finite thickness of the film below the surface plus that of the semi-infinite substrate underneath. 

Figure 9,1 Molecular interaction potentials in Stockmayer s (1941) model for H2O vapor, (a) antiparallel dipolar moments (b) parallel dipolar moments. Reprinted from D. Eisemberg and W. Kauzmann, The Structures and Properties of Water, 1969, by permission of Oxford University Press.

Molecules may vibrate and when they vibrate, their interaction with other molecules is modified. Vibrating molecules often appear bigger and more anisotropic. For selected systems, for example for hydrogen-rare gas pairs, vibrational dependences have been carefully modeled [227]. However, relatively few molecular interaction potentials are well known and for specific cases, one will have to search the recent literature for state of the art models. 

The quantity / is usually called the characteristic length of the interaction potential, and is also employed in the more realistic wave-mechanical treatment. Many authors employ the symbol, a, which is equal to /-1. The form of the molecular interaction potential can be determined in terms of a suitable model, from experimental measurements of the temperature dependence of the viscosity of a gas, whence the characteristic length can be estimated. 

This volume reports the MIF theory, and several applications of MIFs in different arena of the drug discovery process. MIFs are decoding the common language of the (macro)molecules, the molecular interaction potential. Using MIF is simple, interpreting them straightforward. 

Descriptors can be computed from atom coordinates, from the molecular surface [78-80], or from molecular interaction potentials [17, 81, 82]. 

On the other hand, the Kohonen map in Fig. 19 allows only a limited view on similarity because pharmacological profiles of the drugs are not represented correctly. This is because pharmacological properties are not represented by the topological descriptor set. Descriptors based on three-dimensional structures and molecular interaction potentials (hydrogen bonds, lipophihc interactions, steric fit, etc.) are indispensable to describe these properties of molecules. 

For this reason, molecular interaction potentials based on three-dimensional structures are calculated for the compounds of the test dataset. The potentials include all possibibhes of interaction between the small molecule and the en-2ymes, as well as the shape of the molecule. Twenty autocorrelation coefficients are derived from these potentials for each molecule and used as a descriptor set. The new descriptors are mapped in the same way as the topological descriptors by means of a self-organizing map. 

A set of 15 autocorrelation coefficients, calculated from three-dimensional molecular interaction potentials. 

The molecular shape field (MSF) is constituted by values of the molecular interaction potential (MEP) of selected grid points that compose the molecular surface [Urbano-Cuadrado, Carbo et al., 2007]. 

The presence of the metal or insulator does not only add the molecule-substrate interaction as a formative influence, but can also alter the effective intermolecular interactions. For example, whereas the crystallisation of bulk tetraeene is governed by the attractive interaction between molecules in a particular relative orientation, the surface-confined molecules (on Ag( 111)) repel each other. The modification of the effective intermolecular interaction may originate both from substrate-mediation and from the intrinsically anisotropic molecular interaction potentials. As the possibly entropy-driven ordering of tetraeene on Ag(lll) shows, the modified interactions may introduce new ordering mechanisms at the interface. 

H. Weinstein, S. Maayani, and S. Srebrenik, Mol. Pharmacol. 9(6), 820 (1973). Psychotomimetic Drugs as Anticholinergie Agents. II. Quantum-Mechanical Study of Molecular Interaction Potentials of 1-Cyclohexylpiperidine Derivatives with the Cholinergic Receptor. 

Fig. 1.P23. Molecular interaction potential maps for planar (left) and twisted (right)conformations of formamide, 3-aminoacrolein and squaramide.

Complexes of anions with electron-deficient r-tetrazine aromatic rings and other binding units have been studied and compared using both high-level MP2/6-311-l-G ab initio and molecular interaction potential with and without polarization and molecular electrostatic potential calculations, in order to explore the physical nature of the interactions <2003CPL(370)7>. 

GMlPp General molecular interaction potential with polarization... 

In the following we shall make little explieit use of the two factorizations we have here examined, beeause we shall not enter into too teehnieal details about how to obtain accurate molecular interaction potentials. They will be always in the background, however, and some concepts exposed here will be recalled when necessary. 

Focused models may also be used to get more detailed information on the structure of liquids, being in principle more accurate than descriptions solely based on intermolecular potentials. The computational cost is higher, of course, and this approach is now used only at the final stage of the assessment of models of the molecular interaction potential. 

The pure ab initio approach we have summarized has never been used to determine the molecular interaction potentials. Further simplifications are generally used. 

The examination of these high order contributions is addressed in the studies of the mathematical behavior of the separate components of the PT series. Little use has so far been made of them in the actual determination of molecular interaction potentials. 

The numerical output of variational decompositions of AE (supplemented by some PT decompositions) nowadays represents the main source of information to model molecular interaction potentials. In the past, this modeling was largely based on experimental data (supported by PT arguments), but the difficulty of adding new experimental data, combined with the difficulty of giving an interpretation and a decoupling of them in the cases of complex molecules, has shifted the emphasis to theoretically computed values. 

The approach based on discrete descriptions of the solvent makes explicit use of the molecular interaction potentials which may be those defined without consideration of S the calculations are rather demanding of computation time, and this is the main reason explaining why much effort has been spent to have simple analytical expressions of such potentials. 

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