Naked molecule

Schwarz, H. The Chemistry of Naked Molecules or the Mass Spectrometer As a Laboratory. Chem. Unserer Zeit 1991,25, 268-278. 

The fact that only naked molecules are refined is based on the problem that for crystal lattices at least 27 unit cells would have to be included (with at least one unit per cell, including counter ions and solvents of crystallization), and in solution at least 200 molecules of water must be refined in the solvent sheath interacting with the compound to be modeled. Since CPU time f(m2), where m is the number of nuclei, the time required for a single optimization cycle increases dramatically under these conditions. Even more importantly, the initial configuration of the molecule and its environment is not easy to predict since the intermolecular contacts (crystal lattice, ion-pairing and solvation) of a compound to be modeled are not known beforehand. Thus, inclusion of environmental effects in modeling studies has necessitated the use of some severe approximations176-781. 

Optimized structures of naked molecules do not generally differ extensively from crystallographic data. For small organic molecules, bond lengths are reproduced to within 0.005 A and angles are usually accurate to approx. 1°[120 34]. 

The question then is whether and in which cases meaningful results can be expected from the computation of naked molecules. It was pointed out that the relative abundance of an isomer may be related to its elution rate from an ion exchange column12331. This is evidently so because both the abundance and elution rate are related to the stability of the solvated and ion-paired species. Aqueous solutions of chloride, nitrate and perchlorate do not lead to any chromatographic separation of the three isomers of [Co(dien)2]3+[2331. These anions may therefore be... 

The question then is whether, and in which cases, meaningful results can be expected from the computation of naked molecules. It was pointed out that the relative abundance of an isomer may be related to its elution rate from an ion-exchange... 

Tvaroska made a simulation of maltose in various solvents" Based on coordinates gotten from us, he estimated the influence of changing solvent properties on relative conformer populations. One interesting result is that in many solvents a more balanced population is expected than what is calculated for the naked molecule. Our l68... 

Speed manufacturers need only look at the molecules and imagine them without those extra OHs or methylenedioxy ring structures attached to the benzene core. These particular pathways are, however, more uniquely suited for X precursor production because they take advantage of the hindrance that methylenedioxy ring structures and OHs provide on one side of the benzene core. This helps to better assure that mono chloromethylations or bro-minations will occur whereas di- and tri-substitutions are possible on a naked benzene molecule which speed chemists are going to be using (please don t ask). 

The copper system appears to behave similarly to the silver system, and it may be used here in order to illustrate the idea of "selective, naked-cluster cryophotochemistry 150,151). A typical series of optical-spectral traces that illustrate these effects for Cu atoms is given in Fig. 15, which shows the absorptions of isolated Cu atoms in the presence of small proportions of Cu2, and traces of Cus molecules. Under these concentration conditions, the outcome of 300-nm, narrow-band photoexcitation of atomic Cu is photoaggregation up to the Cus stage. The growth-decay behavior of the various cluster-absorptions allows unequivocal pinpointing of UV-visible, electronic transitions associated with Cuj and Cus 150). With the distribution of Cui,2,3 shown in Fig. 15, 370-nm, narrow-band excitation of Cu2 can be considered. Immediately apparent from these optical spectra is the growth (—10%) of the Cu atomic-resonance lines. Noticeable also is the concomitant... 

Figure 19 explains what in principle happens the cluster monolayer on the dendrimer film is mobilized by means of CH2CI2 vapour (a b). The phosphines are then removed by the SH functions (b->c). The bare AU55 nanoclusters move between the dendrimer molecules to form crystals (Auss) which finally appear on the surface (c d). The formation of crystalline superlattices of naked AU55 particles proves their stability which is founded in their perfect cuboctahedral shape. The (Auss) species is a novel modification of the element gold. 

An important consideration for DNA CT in the cell is the dramatically different environment of the DNA molecule in vivo. Unlike the naked DNA typically used in our in vitro assemblies, cellular DNA is intimately associated with proteins, packaged into chromosomes, and stored in the cell nucleus. Several experimental investigations demonstrate definitively that proteins can both modulate and participate in CT reaction in DNA. 

Diffusion is the process by which solute molecules are transported from one part of a system to another as a result of random molecular motion [2], It can be observed with the naked eye when a drop of dye is carefully and slowly placed at the bottom of a beaker filled with water. At first the colored part is separated from the clear by a sharp, well-defined boundary. Later the upper part turns colored, and the color becomes fainter toward the top while the lower part becomes correspondingly less intensely colored. After sufficient time, the whole solution has a uniform color. There is evidently, therefore, a net transfer of dye molecules from the lower part to the upper part of the beaker. The dye molecules have diffused into the water. This diffusion process is primarily due to random molecular motion. 

Polymer crystals consist of well defined arrays of aligned chain segments from adjacent molecules. Polymer crystals (with only a few exceptions) are too small for us to see with the naked eye, or even with an optical microscope. Given their small size, we normally refer to polymer crystals as crystallites . 

Cr(CO)5 interacts with solvent molecules and in solution cannot be considered as naked. The interaction is much weaker with fluorocarbon solvents than hydrocarbon 33). Using a pulsed laser photolysis source (frequency tripled NdYAG) and C7F14 as a solvent, Kelly and Bonneau 33) measured the rate constants for the reaction of Cr(CO)5 with C6H12, CO, and other ligands [Eq. (3)]. 

As discussed above, the solution environment provides for a set of time scales different from the gas phase environment. In solution, there are typically 1013 collisions second"1 of a solute molecule with solvent molecules. Thus, if a photolytically generated species is expected to have a large cross section for reaction with solvent and it is desired to monitor that reaction, both generation and monitoring must be done on a picosecond (psecond) or even sub-psecond timescale. That monitoring this rapid is necessary has been confirmed in an experiment on Cr(CO)6 in cyclohexane solution where psecond photolysis and monitoring was not rapid enough to detect the naked Cr(CO)5 that existed before coordination with cyclohexane (55). 

Other selected examples include tris(tetramethylethylene diamine-sodium)-9,9-dianthryl 143,154 alkali metal salts of 9,10-bis(diisopropylsilyl)anthracene 144,155 as well as the closely related naked 9,10-bis(trimethylsilyl)anthra-cene radical anion 145.156 This chemistry is further extended to the solvent-shared and solvent-separated alkali metal salts of perylene radical anions and dianions 146, 147,156 while other examples focus on alkali metal salts of 1,2-diphenylbenzene and tetraphenylethylene derivatives, where reduction with potassium in diglyme afforded contact molecules with extensive 7r-bonding, [l,2-Ph2C6H4K(diglyme)] 148.157 Extensive 7r-coordination is also observed in (1,1,4,4 tetraphenylbutadiene-2,3-diyl)tetracesiumbis(diglyme)bis(methoxyethanolate) 149.158... 

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