Intermolecular contacts

Inspection of intermolecular contacts can be very informative in pointing at incorrect structures. Obviously, when atoms approach each other closer than the sum of their van der Waals radii there must be either a missed interaction, such as a hydrogen bond, or their positions are in some way in error. Bumping hydrogen atoms may indicate misplaced hydrogen atoms (e.g. two instead of one hydrogen on an sp carbon) or methyl moieties fixed in an inappropriate conformation. 

An interesting case (CSD-entry IDAKUT) where obviously no intermolecular contact analysis was performed is a reported structure with an S—H moiety (Celli et al., 2001). This stracture appears to contain a short S S contact of 2.04 A being clearly a missed S—S bond. The H atom on S should be deleted from this wrongly reported dimeric structure. 

As a rule with few exceptions, OH moieties are hydrogen bonded to an acceptor. Potential H-atom positions lie on a cone. Finding the correct position on this cone can be tricky when the difference electron-density map does not show a single suitable maximum. SHELXL (Sheldrick, 1997b) provides an option to find the optimal position by way of an electron-density calculation around a circle (see Chapter 3 for details). Inspection of contoured difference maps for hydrogen atom positions should be attempted in less obvious settings. 

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Highly linear, unbranched chains allow for maximum interaction between chains. The greater the intermolecular contact between chains, the stronger the forces between them, and the greater the strength of the material. 

It has been pointed out above that, at least for a number of suitable systems, the partial molal volume in solution and the volume occupied by a single molecule in the crystal are practically identical [177]. This finding provides additional support for the applicability of the theoretical models considered. In addition, the intermolecular contacts in the crystal should be similar to the solvation of the complexes in solution. 

The molecules in crystalline chlorine, bromine and iodine are packed in a different manner, as shown in Fig. 11.1. The rather different distances between atoms of adjacent molecules are remarkable. If we take the van der Waals distance, such as observed in organic and inorganic molecular compounds, as reference, then some of the intermolecular contacts in the b-c plane are shorter, whereas they are longer to the molecules of the next plane. We thus observe a certain degree of association of the halogen molecules within the b-c plane (dotted in Fig. 11.1, top left). This association increases from chlorine to iodine. The weaker attractive forces between the planes show up in the plate-like habit of the crystals and in their easy cleavage parallel to the layers. Similar association tendencies are also observed for the heavier elements of the fifth and sixth main groups. 

Figure 11 Potential hydrogen bond partners to the backbone atoms of the inhibitor and the residues of the S/ subsite that are in intermolecular contact with the Pi homophenylalanine.

The carbon atoms which are involved in the short intermolecular contacts between molecules (less than 4A 02/C14 and 01/C4, C5, C6, Figure 7) carry a significant spin density. The magnetic molecular orbitals of the corresponding oxygen atoms (01 and 02) are twisted and hybridized. Thus we have evidence that the intermolecular exchange involves these contacts. 

An intermolecular analog of this inter-ring pnictogen bonding is found in the thermochromic distibines and dibismuthines.45 For example, 2,2, 5,5 -tetramethylbistibole (87) crystallizes so that the Sb atoms are aligned in chains with close contacts between the Sb atoms of adjacent molecules. It seems more than coincidental that the intermolecular contacts in 87 occur at virtually the same distance as the intramolecular contacts in 29. See Figure 3. 

Fig. 2 Representation of the ferromagnetic alignment of d localized spins resulting from the interaction with itinerant electrons through short intermolecular contacts...

Second, the spin density maps must cover the atoms which are involved in the contacts. On the one hand, the localized d spins of the transition metal ions must paradoxically be sufficiently delocalized toward the ligand atoms. On the other hand, the n carriers of the donor set have to extend toward the peripheral atoms. In fact the electrons belonging to the two networks must meet at the intermolecular contact, otherwise the networks would ignore each other. 

Fig. 3 Structural arrangement in (DIET)2[Crm(isoq)2CNCS)4] (phase a) of the inorganic and organic moieties showing the one-dimensional arrays and the remarkably short intermolecular contacts (thin gray line) between iodine-substituted donors and sulfur atoms of the isothiocyanato ligands...

The structurally related salts [M(Cp )2] [M (tds)2] (M = Fe, Mn, Cr M = Ni, Pt) and [Fe(Cp )2][Pt(tds)2] allowed a systematic study of the effect of a diversity of variables on the magnetic behavior of these compounds, such as the variation of the spin of the cation, the role of the single ion anisotropy, the effect of the variation of the size of atoms involved in the intermolecular contacts. Furthermore, the analysis of the intermolecular contacts in these compounds provided a reasonable interpretation of the intra and interchain magnetic coupling, and its relative strength within the series [44, 45]. 

The compound [Fe(Cp )2][Ni(a-tpdt)2], although not isostructural with the [Cr(Cp )2] analogue, presents a lower symmetric structure, where one of the crystallographic axis is doubled. This axis doubling is associated with a slight alternation in the D+-A contacts along the chains and consequently also in interchain contacts. Otherwise the network of intermolecular contacts remains similar. There are no full structural refinements for the other compounds of this series but the unit cell parameters of the (M = Fe, M = Au) compound and powder diffraction data of the salt with M = Co, M = Ni indicate that they are isostructural with the M = Fe, M = Ni compound. On the other hand, powder diffraction data on the M = Mn, M = Ni compound indicate that it is isostructural with the M = Cr, M = Ni compound. 

The complexity of the crystal structure of the [M(Cp )2][M (bdt)2] salts and the large number of intermolecular contacts in this series of complexes prevents a clear interpretation of the magnetic behavior and a correlation between the crystal structures and the magnetic properties. However, the saturation magnetization value in the case of the compounds [Mn(Cp )2][M (bdt)2] (M = Ni and Pt) is consistent with a D+A- AF coupling. A similar coupling is expected to occur in [Fe(Cp )2][M (bdt)2] (M = Ni and Pt), where %T shows a similar behavior, typical of a FIM above the ordering temperature. 

A singlet-triplet behavior is found for those complexes such as [CpNi(oxdt)] [71]or [CpNi(F2pdt)] [72] associated into dyads (Fig. 12), where the strong distortions from planarity of the dithiolate ligands hinder any other interdyad intermolecular contacts. The large Ni S and S S intermolecular distances lead to weak intermolecular interactions with / values of —29 or —8 cnC1 for [CpNi(oxdt)] and [CpNi(F2pdt)] respectively. 

The X-ray crystal structure of 6-chloro-2,3-dihydro-7-methyl-5-methyIene-2//, 3H, 5H- l,4-dithiepin-l,l,4,4-tetraoxide has been published and a short intermolecular contact across an inversion centre noted <00AX(Qel09>. An experimentally direct and efficient approach to 1,3-dithiepins has been reported using 1 qi-alkyldihalides and carbon disulfide and sodium borohydride, to generate the sulfide nucleophile . 

Mass spectrometric studies indicate that smaller molecule derivatives such as Bi(SCMe3)3 are monomeric in the gas phase (33), and the solid-state structure of Bi(SC6H2 6118-2,4,6)0 reveals a pyramidal environment for bismuth [S-Bi-S 90.3(2) to 104.5(2)°] with uniform Bi-S distances [Bi-S 2.554(7) to 2.569(8) A], However, the absence of intermolecular contacts is likely enforced by the steric bulk of the... 

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