Really big molecules

From alkylthio-derivatives of bi-TTF tetraalkylthio-bi-TTF can be obtained using the phosphite-mediated cross-coupling method (strategy S2). Depending on the solvent, an intermediate molecule is obtained whose homocoupling yields the tetraalkylthio-tri-TTF (see Fig. 2.14). 

Oligomerization leads to large molecules such as dendrimers, macrocycles, cy-clophanes, etc. The ability to build growing molecules has also led to covalent 

Ceo-TTF molecules, interlocked molecules (catenanes, rotaxanes), donor-acceptor macrocycles, cage molecules, etc. (Jeppesen et al, 2004). It is beyond the scope of this book to review such developments and I appeal to the curiosity of researchers really not familiar with such macromolecules to see how big the molecules can become. 

One astute way to obtain macrocyclic systems with TTF is the stepwise method of deprotection/alkylation of cyanoethyl-protected TTF-thiolates. With this method molecular units can be built but with the precaution of preserving one cyanoethyl group in order to be able to iteratively proceed with the oligomerization. Combining such units, larger units can be produced. An example of a TTF dendrimer containing 21 TTFs is shown in Fig. 2.15 (Christensen et al, 1998). Here only the main philosophy of the synthesis is discussed. 

The starting cyanothioethyl thiolate molecule (a) is converted to the thione (b) and coupling of (b) with (c) yields the fundamental TTF-derivative brick (d). Reaction with (e) renders (f) and the iterative reaction of (f) with (d) gives larger molecules such as (g). Indeed the correct experimental conditions have to be met for each step. As pointed out above, it is mandatory in order to proceed with the dendrimerization to preserve the cyanoethyl hook. 

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In calculating the metallic surface area, one has to take proper care of the reaction stoichiometry. In the ideal case, a molecule occupies one site, as shown for terminal adsorbed CO in Fig. 3.46.a. Alternatively, a molecule may chemisorb on more than one metal atom, as shown in Fig. 3.46.b and c for bridged-site adsorbed CO and in Fig. 3.46.d for valley-site adsorbed CO, respectively. In some specific cases of really big molecules, one can imagine that a molecule adsorbs on only one site, while simultaneously blocking adjacent sites for geometric reasons. In case an adsorbate molecule adsorbs dissociatively, it will occupy more than one site as shown in Fig. 3.46.e. 

Final question how big are the nucleic acids How many nucleotide units do we typically find in DNA or RNA The answer is enormously variable. There are small RNA molecules that contain 25 or fewer nucleotides there are also RNA molecules that contain thousands of nucleotides. But for really, really big molecules, we turn to DNA, which may have tens of thousands of nucleotides linked together Specific examples follow below but we need some additional insights first. 

No, and this is another way that chemists classify these really big molecules. The major types of polymer shapes (technical term topology) are linear, branched, and crosslinked networks. Linear polymers are chains of monomers joined together, like a noodle or a rope. If there is a point along a polymer chain where a second chain starts, like a fork in the road, this arrangement is referred to as branched. 

Big molecules of life include the proteins, nucleic acids, polysaccharides, and a few other more exotic constrncts of nature. Generally, it is the interactions between big molecules and small ones that nnderlie really interesting things taste or smeU or the beneficial actions of drugs, for example. 

There are big molecules (proteins, nucleic acids) and small molecules (most of the rest). The really interesting stuff happens when big molecules and small molecules interact to produce some biological action. 

A single drop of water contains about 10 molecules. There are a lot of drops of water in the world s oceans. These contain about 10" molecules of water, a really big number ... 

If we now incorporate functional groups in the CeHe-based molecules we will have important molecules such as CA, DMe-DCNQI, TCNQ, TMPD, TNAP and ITT, but the really big jump is encountered when pentagons are allowed to be included. The possibilities to build new molecules become even more numerous than with only CeHe pieces, although we already had an immense number... 

Space-filling model kits are even less user friendly. They employ specially shaped atomic pieces that clip together, each representing the volume taken up by the atom and its bonding electrons. This system produces a rather more globular model that indicates the whole bulk of the molecule, including the electron clouds that are involved in bonding. The value of this type of model is that it shows just how big the molecule really is, and... 

Market conditions (available candidates versus available openings), not to mention talent, experience, and luck, will dictate how much of a choice of potential employers the candidate will really have. Still, it s always a good idea to picture what an ideal situation would be as a benchmark to compare real opportunities with. Industrial research on small molecule therapeutics can take place in big pharma or at smaller companies, which may be called biotechs whether or not they also try to develop biologies. The alternative term, small pharma might also describe them, as we ve seen. 

The cluster approach was, for a long time, the only available mechanism for calculating NMR parameters. A crystalline system can be, up to some extent, approximated as a cluster of units (molecules/ions/atoms) whose configuration resembles the crystal. The local environment in the center of this cluster is then an approximation to the bulk solid. The resemblance of the cluster with the true crystal tends to increase as the size of the cluster grows. Therefore, the size of the cluster is critical for the accurate calculation of the desired parameters, as small clusters do not really mimic the crystal environment, whereas big clusters imply heavy computational burdens. When using this approach, the optimal choice resides in a tradeoff between accurate crystal description and acceptable computational cost. 

What really react therefore to justify a so big dependence with temperature Arrhenius assumed the existence of a new specimen in the reaction the active sugar. It is the number of molecules of active sugar that determine the velocity of reaction, they are the true reacting species. There is another subordinate equilibrium inside the reaction between sugar and active sugar that determinate its kinetic... 

How big should the box be If it is a cube, and we want to put a moderately-sized solute molecule in it, a box with 5 A sides would be too small—solute molecules might protrude out of the box. A 100 A box would be much better, but really very large in terms of computation. For small organic solutes, a cube with 20 A sides is often adequate. It is a simple matter to calculate that 267 water molecules will fit into a 20 X 20 X 20 A box. If the solute is ethane, for example, it would take the place of two waters, based on its size. Thus, our calculation would be on a box with 265 water molecules and one ethane. 

We want to solve the molecular Schrodinger equation. No, really, we do, because the resulting energies and wavefunctions will predict the behavior of molecules in situations that we care about in all branches of chemistry why the molecule has the spectrum it has, whether it forms a liquid or solid or gas, why it reacts the way it does. The molecular Hamiltonian unlocks the whole world of chemistry. But it s a big world, and we re going to travel it in steps, beginning with how the Coulomb force dictates the shape of the potential energy term. 

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