Bonding potentials

Gavezzotti A and Filippini G 1994 Geometry of the intermolecular XH.. . Y (X,Y = N,0) hydrogen bond and the calibration of empirical hydrogen-bond potentials J. Phys. Chem. 98 4831... 

Wiliams D E 1965 Non-bonded potential parameters derived from crystalline aromatic hydrocarbons J. Chem. Phys. 45 3770... 

Figure C2.5.7. The native confonnation of fast folding sequence (N= 27) witli random bond potentials is shown. This stmcture has c = 22 non-bonded contacts, tlierefore it is not a maximally compact confonnation for which c = 28. The figure was created using RasMol 2.6 [8].

The representation of molecules by molecular surface properties was introduced in Section 2.10. Different properties such as the electrostatic potential, hydrogen bonding potential, or hydrophobicity potential can be mapped to this surface and seiwe for shape analysis [44] or the calculation of surface autocorrelation vectors (refer to Section 8.4.2). 

AMorse function best approximates a bond potential. One of the obvious differences between a Morse and harmonic potential is that only the Morse potential can describe a dissociating bond. 

The AMBER force field replaces the van der Waals by a 10-12 potential for pairs of atoms that can participate in hydrogen bonding (equation 12). The hydrogen bond potential does not contribute significantly to the hydrogen bonding attraction between two atoms rather, it is implemented to fine-tune the distances between these atoms. 

Force field calculations often truncate the non bonded potential energy of a molecular system at some finite distance. Truncation (nonbonded cutoff) saves computing resources. Also, periodic boxes and boundary conditions require it. However, this approximation is too crude for some calculations. For example, a molecular dynamic simulation with an abruptly truncated potential produces anomalous and nonphysical behavior. One symptom is that the solute (for example, a protein) cools and the solvent (water) heats rapidly. The temperatures of system components then slowly converge until the system appears to be in equilibrium, but it is not. 

For thin-film samples, abrupt changes in refractive indices at interfrees give rise to several complicated multiple reflection effects. Baselines become distorted into complex, sinusoidal, fringing patterns, and the intensities of absorption bands can be distorted by multiple reflections of the probe beam. These artifacts are difficult to model realistically and at present are probably the greatest limiters for quantitative work in thin films. Note, however, that these interferences are functions of the complex refractive index, thickness, and morphology of the layers. Thus, properly analyzed, useful information beyond that of chemical bonding potentially may be extracted from the FTIR speara. 

We often refer to Heitler and London s method as the valence bond (VB) model. A comparison between the experimental and the valence bond potential energy curves shows excellent agreement at large 7 ab but poor quantitative agreement in the valence region (Table 4.3). The cause of this lies in the method itself the VB model starts from atomic wavefunctions and adds as a perturbation the fact that the electron clouds of the atoms are polarized when the molecule is formed. 

Although cross terms between the bonded potentials are part of all force fields designed to aclfieve high accuracy, the coupling between the geometry and the atomic charges is rarely addressed. From electronic structure calculations it is known that the optimum set... 

Bonding Potentially better layers are in contact longer in die ... 

In 1936, de Boer formulated his theory of a stressed bond which, despite its simplicity, still constitutes the basis for most models of chemical reactivity under stress [92], In order to fracture an unstressed bond which, in the absence of any vibration, is approximated by the Morse potential of Fig. 18, an energy D must be supplied. If, however, the bond is under tension due to a constant force feitt pulling on either end, the bond rupture activation energy will be decreased by an amount equivalent to the work performed by the mechanical force over the stretching distance from the equilibrium position. The bond potential energy in the presence of stress is given by ... 

It will be assumed for the moment that the non-bonded atoms will pass each other at the distance Tg (equal to that found in a Westheimer-Mayer calculation) if the carbon-hydrogen oscillator happens to be in its average position and otherwise at the distance r = Vg + where is a mass-sensitive displacement governed by the probability distribution function (1). The potential-energy threshold felt is assumed to have the value E 0) when = 0 and otherwise to be a function E(Xja) which depends on the variation of the non-bonded potential V with... 

H H non-bonded interactions are of great importance in organic compoimds, and thus it was of interest to attempt to investigate H H non-bonded potential functions via the determination of a steric isotope effect in the configurational inversion of an unsubstituted biaryl. In view of the extensive work of Harris and her co-workers in the 1,1 -binaphthyl series (see, for example, Badar et al., 1965 Cooke and Harris, 1963), and since the parent compound is one of the simplest hydrocarbons that may be obtained in enantiomeric forms, the determination of the isotope effect in the inversion of l,l -binaphthyl-2,2 -d2 (9) was... 

The anharmonic modes for both the a symmetric and 67 asymmetric CH stretching vibrations have been explored. In order to perform a reasonable anharmonic treatment, we had to take into account the stretching of the bonds to larger elongations than for the harmonic description where displacements can be confined close to the equilibrium geometry. Consequently, correlation effects were included in the determination of the potential surface. The electronic calculations were carried out at the MP2 level, which insures a good description of the CH bond potential towards dissociation. A double zeta... 

Rey, S., Caron, G., Ermondi, G., Gaillard, P., Pagliara, A., Carrupt, P. A., Testa, B. Development of molecular hydrogen bonding potentials (MHBPs) and their application to structure-permeation... 

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