Effective distance-dependent

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

Distance-dependent dielectric constant In computing the Coulomb interaction between two point charges, the dielectric constant is set to the value of the dielectric medium. In an attempt to implicitly simulate water, the dielectric constant should be 80 at long distances, but 1 at close range. Replacing the dielectric constant by r makes the dielectric effect distance-dependent at negligible computational cost. 

Use Equation VIII-1 to determine the effective mass of the cantilever if the cantilever has a spring constant C = 20 N/m, the minimum detectable force gradient is hF/dz = 4 X 10 N/m, and the frequency shift is 200 kHz. How does the frequency shift depend on distance from the surface if the force has a 1/z distance dependence ... 

R), i.e. there is no effect due to caging of the encounter complex in the common solvation shell. There exist numerous modifications and extensions of this basic theory that not only involve different initial and boundary conditions, but also the inclusion of microscopic structural aspects [31]. Among these are hydrodynamic repulsion at short distances that may be modelled, for example, by a distance-dependent diffiision coefficient... 

In this model of electrostatic in teraction s, two atoms (i and j) have poin t charges tq and qj. The magnitude of the electrostatic energy (V[. , [ ) varies inversely with the distance between the atoms, Rjj. fh e effective dielectric constant is . For in vacuo simulations or simulation s with explicit water rn olecules, the den om in a tor equals uRjj, In some force fields, a distance-dependent dielectric, where the denominator is uRjj Rjj, represen is solvent implicitly. 

In a second attempt to obtain more insight into the binding location of the dienophile and now also the diene, we have made use of the influence of paramagnetic ions on the spin-lattice relaxation rates of species in their proximity. Qose to these ions the spin-lattice relaxation rate is dramatically enhanced. This effect is highly distance-dependent as is expressed by Equation 5.7, describing the spin-lattice... 

A distance-dependent dielectric constant is commonly used to mimic the effect of solvent in molecular mechanics calculations, in the absence of explicit water molecules. 

Also use constant dielectric for MM+ and OPLS calculations. Use the distance-dependent dielectric for AMBER and BlO-t to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, 8, can vary from 1 to 80. HyperChem sets 8 to 1.5 for MM-t. Use 1.0 for AMBER and OPLS, and 1.0-2.5 for BlO-t. 

The hazard posed can be limited by maintaining a zone free of people and property around a storage area of explosive material. The minimum radius of the zone depends on the type and quantity of explosive, the extent and type of barrica ding, and the magnitude of loss that would be encountered if an explosive incident occurred. The maximum distance to which hazardous explosive effects propagate depends on the blast overpressure created, which as a first approximation is a function of the cube root of the explosive weight, W. This is termed the quantity distance and is defined as... 

These simple velocity profiles do not indicate directly any dependence of the flow pattern efficiency upon the rotational speed of the centrifuge. A dependence on speed is to be expected on the basis of the argument that at high speeds the gas in the centrifuge is crowded toward the periphery of the rotor and that the effective distance between the countercurrent streams is thereby reduced. It can be seen from the two-sheU model that, as the position of upflowing stream approaches the periphery, the flow pattern efficiency drops off from its maximum value. 

Entrance and Exit Effects In the entrance region of a pipe, some distance is required for the flow to adjust from upstream conditions to the fuUy developed flow pattern. This distance depends on the Reynolds number and on the flow conditions upstream. For a uniform velocity profile at the pipe entrance, the computed length in laminar flow required for the centerline velocity to reach 99 percent of its fully developed value is (Dombrowski, Foumeny, Ookawara and Riza, Can. J. Chem. Engr, 71, 472 76 [1993])... 

Composilion has a marked effect on p. Dilution can cause (i to drop by orders of magnitude. The functional dependence is often expressed in terms of an exponential dependence on intersite distance R=at m as suggested by the homogeneous lattice gas model, p c)exponential distance dependence of intersite coupling precludes observing a percolation threshold for transport. 

Although the DMT theory attempts to incorporate distance-dependent surface interactions into the adhesion problem, it does not take into account the effect surface forces have on the elastic deformation. In other words, it does not predict the neck formation predicted by JKR. 

BLEVEs/Pressure-volume Ruptures/Physical Explosions. Rapid loss of containment of materials confined under pressure at temperatures above their normal boiling point may result in a BLEVE, with blast, radiant heat (if flammable material is involved), as well as fragment effects. These effects can be experienced for considerable distances, depending upon the types and volumes of material stored. 

As is apparent from the above definitions, each of these effective matrices depend on basis sets and molecular orbitals of both fragments. It is also important to observe that these matrices possess a correct asymptotic behavior as at large interfragment distances they become the usual overlap and Fock matrices of the separate fragments, while the paired secular systems uncouple and converge to the separate Roothaan equations for the single monomers. Finally, as it is usual in a supermolecular approach, the interaction energy is expressed as... 

This step is important in that it prevents the large-amplitude oscillations (typically present at low k) from dominating over the smaller ones (typically at high k). This is critical since the determination of interatomic distances depends on the frequency and not the amplitude of the oscillations. Other approaches having the same effect have also been employed.37,47... 

Evaluation of trends in /pp coupling constants in solid-state 31P NMR spectra of P-phospholyl-NHPs allowed one to establish an inverse relation between the magnitude ofM and P-P bond distances [45], The distance dependence of. /pp is in line with the dominance of the Fermi contact contribution, and is presumably also of importance for other diphosphine derivatives. At the same time, large deviations between lJvv in solid-state and solution spectra of individual compounds and a temperature dependence of lJ77 in solution were also detected (Fig. 1) both effects... 

An alternative approach is that adopted by Horrocks and co-workers, where the aromatic residues in metal-binding proteins are used as sensitizers. Since the distance between the metal and the donor is effectively fixed, this provides a rigid scaffold for the experiment, and the absence of a directly conjugated pathway between the metals means that Forster (through space) energy transfer can be assumed. The r-6 distance-dependence of this means that the extent of sensitized emission from the lanthanide ion provides information on the spatial relationship between the metal-ion binding site (lanthanide ions often bind at Ca2+ sites) and nearby aromatic residues. 58-60... 

The effective CF models, intended to include covalence effects via effective charges and shielding parameters [46] (superposition model [47], effective charge model [48], simple overlap model [49, 50]), keep the radial (M-L distance) dependence of the CF parameters as in the simple (point charge) electrostatic model. Dedicated studies have shown, however, that the radial dependence of these parameters deviates strongly from the latter for the whole series of lanthanide ions [51, 52]. 

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