Distance contact

Th eri water mo Iccu les are elim in ated if an y of th c Lh rce atom s arc closer to a solute atom than the contact distance you specify. 

Prior to solvation, the solute is oriented according to its inertial axes such that the box size needed to accommodate it is minimized (minimizing the number of water molecules). The principal inertial axis is oriented along the viewer s Z axis, for example. Then water molecules are eliminated if any of the three atoms are closer to a solute atom than the contact distance you specify. 

When two atoms approach each other so closely that their electron clouds interpenetrate, strong repulsion occurs. Such repulsive van der Waals forces follow an inverse 12th-power dependence on r (1/r ), as shown in Figure 1.13. Between the repulsive and attractive domains lies a low point in the potential curve. This low point defines the distance known as the van der Waals contact distance, which is the interatomic distance that results if only van der Waals forces hold two atoms together. The limit of approach of two atoms is determined by the sum of their van der Waals radii (Table 1.4). 

In realgar the short non-bonding contact distances are 3.3 A for sulfur-sulfur, 3.6 A for sulfur-arsenic, and 3.5 A for arsenic-arsenic. They are accordingly about 1.2 A greater than the corresponding single-bond lengths, as found in other crystals. 

The way forward was proposed by Berne and Pechukas [11] many years later. Their important idea was to consider the overlap between two prolate ellipsoidal gaussian distributions. From the expression for this overlap they evaluated a range parameter which was taken to be the contact distance g and a strength parameter which was set equal to the well depth, e. If the orientations of the two rod-like molecules in the laboratory frame are represented by the unit vectors Ui and Uj and the orientation of the intermolecular vector by the unit vector f then the expression for the angular dependence of the contact distance is... 

It is of interest to note that in this model the anisotropy in the attractive energy is determined by the same parameter, 7, as that controlling the anisotropy in the repulsive energy. In these expressions for the contact distance and the well depth their angular variation is contained in the three scalar products Uj Uj, Uj f and uj f which are simply the cosines of the angle between the symmetry axes of the two molecules and the angles between each molecule and the intermolecular vector. 

Here, the tilde indicates the parameter for the combination of a rod-like molecule and an atom so denotes the contact distance when the atom is at the end of the molecule and dj that when it is at the side. The analogous expression used for the well depth is... 

The investigated solid phase of 5SCN crystallises in the monoclinic space group P2i/c with 12 molecules per unit cell [109]. The three crystallograph-ically independent molecules are in an extended form. The molecules are arranged parallel to the (001) plane. The averaged contact distances between the cyano groups of adjacent molecules are 3.58 A Ncya o-N cyano> 3.52 A... 

Table 1 Contact distances predicted by the anisotropic model [56] (reproduced from ref [15], with permission of the ACS)...

The structure of iodine at four different pressures. The outlined face-centered unit cell in the 30-Gpa figure corresponds to that of a (distorted) cubic closest-packing of spheres. At 24.6 GPa four unit cells of the face-centered approximant structure are shown the structure is incommensurately modulated, the atomic positions follow a sine wave with a wave length of 3.89 x c. The amplitude of the wave is exaggerated by a factor of two. Lower left Dependence of the twelve interatomic contact distances on pressure... 

Tellurium crystallizes isotypic to a-selenium. As expected, the Te-Te bonds in the chain (283 pm) are longer than in selenium, but the contact distances to the atoms of the adjacent chains are nearly the same (Te- Te 349 pm). The shortening, as compared to the van der Waals distance, is more marked and the deviation from a regular octahedral coordination of the atoms is reduced (cf. Table 11.1, p. 111). By exerting pressure all six distances can be made to be equal (cf. Section 11.4). 

R. S. Rowland, R. Taylor, Intermolecular nonbonded contact distances in organic crystal structures. J. Chem. Phys. 100 (1996) 7384. 

Eo and E (Afi(i)) are respectively the electric fields generated by the permanent and induced multipoles moments. a(i) represents the polarisability tensor and Afi(i) is the induced dipole at a center i. This computation is performed iteratively, as Epoi generally converges in 5-6 iterations. It is important to note that in order to avoid problems at the short-range, the so-called polarization catastrophe, it is necessary to reduce the polarization energy when two centers are at close contact distance. In SIBFA, the electric fields equations are dressed by a Gaussian function reducing their value to avoid such problems. 

H). As shown, a disordered structural model was obtained for the guest. The model comprises two mirror-related guest molecules. The oxygen atom and the proximal methyl C-atom are practically overlapping the same atomic positions in both orientations. However, the sulphur atomic positions do not average in the X-ray data and show a nearly 50/50 occupancy. As indicated by the comparison of the respective bond distances and intra-associate contact distances of the DMSO molecule (Table 17), the effect of disorder is serious (e.g. the S=0 distances appear abnormally short in the 20 DMSO instance). This precludes the possibility of assessing interaction between the O atom of the carboxyl and a methyl of dimethyl sulfoxide. 

Figure 5.2 (a) Electron density contour map of the CI2 molecule (see Chapter 6) showing that the chlorine atoms in a CI2 molecule are not portions of spheres rather, the atoms are slightly flattened at the ends of the molecule. So the molecule has two van der Waals radii a smaller van der Waals radius, r2 = 190 pm, in the direction of the bond axis and a larger radius, r =215 pm, in the perpendicular direction, (b) Portion of the crystal structure of solid chlorine showing the packing of CI2 molecules in the (100) plane. In the solid the two contact distances ry + ry and ry + r2 have the values 342 pm and 328 pm, so the two radii are r 1 = 171 pm and r2 = 157, pm which are appreciably smaller than the radii for the free CI2 molecule showing that the molecule is compressed by the intermolecular forces in the solid state. 

Figure 5.11 Bond angles and intramolecular contact distances in AX3E and AX4 molecules.

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