Stacked molecules

Myosin is quantitatively the most important protein in the myofibrils, representing 65% of the total. It is shaped like a golf club (bottom right). The molecule is a hexamer consisting of two identical heavy chains (2 X 223 kDa) and four light chains (each about 20 kDa). Each of the two heavy chains has a globular head at its amino end, which extends into a tail about 150 nm long in which the two chains are intertwined to form a superhelix. The small subunits are attached in the head area. Myosin is present as a bundle of several hundred stacked molecules in the form of a thick myosin filament. The head portion of the molecule acts as an ATPase, the activity of which is modulated by the small subunits. 

The strongly colored planar fused bicyclic system (25) is quinonoid with distinctly alternating bond lengths 1.33-1.35 A and 1.42-1.44 A. A strong 7r-stacking interaction in the molecule (28) between tolyl and phenanthroline planes is evident (interplane distance is 3.3 A), as well as between tolyl and cyclopentadienyl planes (the distance is 3.61 A) which results in columns of stacked molecules. 

The study of vapour-deposited organic films has been applied to a large number of molecular systems. However, most of the work has concentrated on the study of the growth and optoelectronic characteristics of planar stacking molecules such as the Pc and polycyclic aromatic compounds based on naphthalene, and perylene. In particular, PTCDA has become extensively studied. 

It is constructive at some point to carefully define the difference between the various types of electronic states that arise when two molecules are brought into close contact, as in the case of the stacked bases in a DNA chain. Let us consider a simple model for understanding the various excited state configurations that can arise between stacked molecules. For the sake of simplicity, consider the following 4 electronic configurations ... 

A number of anthracene derivatives have been prepared that take advantage of this approach. Two excellent examples are 9-nitroanthracene (9) [23] and anthryl trifluoromethyl ketone (10) [24], Both of these molecules, with strongly electron-withdrawing groups, adopt a nearly columnar it-stacked arrangement in the crystal (Fig. 14.7). The separations between the it-faces of these stacked molecules (the parameter with the most dramatic impact on charge transport [7]) are 3.53 A (9) and 3.56 A (10). 

As the size of the substituents on the central carbon atoms is increased, the longitudinal (long-axis) and lateral (short-axis) slip of the stacked molecules also increases, until a solid-state arrangement with coplanar anthracene rings that do not overlap is achieved. This arrangement is best exemplified by the well-known 9,10-diphenylanthracene (16) (Fig. 14.11) [30],... 

AMI semiempirical calculations have shown that, as far as tautomerism is concerned, there is a structural relationship between jS-dicarbonyl compounds and NH-pyrazoles, and in a wide variety of NH-pyrazoles studied " the most stable tautomer was found to be that having the largest single-bond character between the C(3)—C(4) bond. The problem of proton transfer in NH-pyrazole crystals has been subjected to a detailed theoretical study, while a study of the tautomerism of 2-aryl and 2-heteroaryl derivatives of benzimidazole has indicated that tautomerism takes place by the intermolecular relay of protons between stacked molecules. The first report of the stable co-existence of two different histidine tautomers in one peptide crystal structure has appeared. Ab initio calculations have been used to study the tautomerism of both histamine and pyrazolo[3,4-i/]pyridazine in the gas phase and in aqueous solution, and a theoretical study of the NH tautomerism in free-base porphyrin has been undertaken. ... 

Table FV. Structure parameters obtained from EXAFS analysis of [Ni (CgO)4dpg 2] at different temperatures. ( ) means the atoms of neighboring stacking molecules.

Assume that the sample contains a mixture of charged particles. When these are in an electrical field in a narrow channel, they tend to stack vertically. A liquid flowing through the channel has a parabolic flow profile. The molecules near the center of the channel are pushed by a faster flow than those near the edge, and this results in a separation. Any field that stack molecules or particles can be used, and the particles need not be charged. This includes heat and centrifugal force. 

FIGURE 1.1.3 Illustration of the bonding-antibonding interactions between the HOMO/ LUMO levels of two ethylene molecules in a cofacial configuration we also illustrate the formation of the valence and conduction bands when a large number of stacked molecules interact. 

FIGURE 5.2.13 A model for the aggregation of HT-PHT in the colloidal solntion solvent = mixture of CHClj and CHjOH. The aggregate may consist of several snbnnits with the side-to-side stacked molecules. (Yamamoto, T. et al., J. Am. Chem. Soc., 120(9), 2047, 1998. With... 

Other complex structures which show similar packing arrangements based on charge-transfer interactions include the 1 1 complexes of mesitylene-hexafluorobenzene, thymine-p-benzoquinone, and the 1 2 complex formed by phlorogludnol and p-benzoquinone. The mesitylene complex consists of alternately stacked molecules of mesitylene and hexa-fluorobenzene [separation 3.56 A]. There are also nearly linear C-H F [3.24 A] intermolecular contacts, and the possibility of methyl-fluorine hydrogen-bonding cannot be discounted. The structures of both the thymine and phlorogludnol complexes with p-benzoquinone may be described In... 

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