Compact molecules

Compactness. Given the size of today s databases and the requirement to store hundreds of conformers per molecule, compactness of storage becomes an issue with respect to both file size and retrieval efficiency. 

The molecule in part (b) is cholesterol, which is drawn in two different manners. In the upper drawing, we show all the C s and H s, and one can easily identify the different modular fragments that constitute this molecule. In the lower drawing, we remove all atom labels, except for the OH group. This is the concise representation that organic chemists use to depict their molecules compactly without the forest of C s and H s. By consent, every chemist understands that what is drawn in Scheme 5.3b is the carbon skeleton of the molecule, wherein a terminal carbon represents CH3, a... 

Under certain conditions of temperature and pressure, and in the presence of free water, hydrocarbon gases can form hydrates, which are a solid formed by the combination of water molecules and the methane, ethane, propane or butane. Hydrates look like compacted snow, and can form blockages in pipelines and other vessels. Process engineers use correlation techniques and process simulation to predict the possibility of hydrate formation, and prevent its formation by either drying the gas or adding a chemical (such as tri-ethylene glycol), or a combination of both. This is further discussed in SectionlO.1. 

Technology developments are revolutionizing the spectroscopic capabilities at THz frequencies. While no one teclmique is ideal for all applications, both CW and pulsed spectrometers operating at or near the fiindamental limits imposed by quantum mechanics are now within reach. Compact, all-solid-state implementations will soon allow such spectrometers to move out of the laboratory and into a wealth of field and remote-sensing applications. From the study of the rotational motions of light molecules to the large-amplitude vibrations of... 

The systematic lUPAC nomenclature of compounds tries to characterize compounds by a unique name. The names are quite often not as compact as the trivial names, which are short and simple to memorize. In fact, the lUPAC name can be quite long and cumbersome. This is one reason why trivial names are still heavily used today. The basic aim of the lUPAC nomenclature is to describe particular parts of the structure (fi agments) in a systematic manner, with special expressions from a vocabulary of terms. Therefore, the systematic nomenclature can be, and is, used in database systems such as the Chemical Abstracts Service (see Section 5.4) as index for chemical structures. However, this notation does not directly allow the extraction of additional information about the molecule, such as bond orders or molecular weight. 

The first line notations were conceived before the advent of computers. Soon it was realized that the compactness of such a notation was well suited to be handled by computers, because file storage space was expensive at that time. The heyday of line notations were between I960 and 1970, A chemist, trained in this line notation. could enter the code of large molecules faster than with a structure-editing program,... 

Fingerprints structural keys identify a molecule - code is highly compact represented in bits ambiguous not convertible to other representations dependent on the fragment library... 

A SMILES code [22], MDL Molfile [50], or JME s own compact format (one-line representation of a molecule or reaction including the 2D coordinates) of created molecules may be generated. The created SMILES is independent of the way the molecule was drawn (unique SMILES see Section 2.3.3). Extensions to JME developed in cooperation with H. Rzepa and P. Murray-Rust also allow output of molecules in the CML format [60]. 

To be specific let us have in mind a picture of a porous catalyst pellet as an assembly of powder particles compacted into a rigid structure which is seamed by a system of pores, comprising the spaces between adjacent particles. Such a pore network would be expected to be thoroughly cross-linked on the scale of the powder particles. It is useful to have some quantitative idea of the sizes of various features of the catalyst structur< so let us take the powder particles to be of the order of 50p, in diameter. Then it is unlikely that the macropore effective diameters are much less than 10,000 X, while the mean free path at atmospheric pressure and ambient temperature, even for small molecules such as nitrogen, does not exceed... 

An alternative way to represent molecules is to use a linear notation. A linear notation uses alphanumeric characters to code the molecular structure. These have the advantage of being much more compact than the connection table and so can be particularly useful for transmif-ting information about large numbers of molecules. The most famous of the early line notations is the Wiswesser line notation [Wiswesser 1954] the-SMILES notation is a more recent example that is increasingly popular [Weininger 1988]. To construct the Wiswesser... 

Molecular orbitals are useful tools for identifying reactive sites m a molecule For exam pie the positive charge m allyl cation is delocalized over the two terminal carbon atoms and both atoms can act as electron acceptors This is normally shown using two reso nance structures but a more compact way to see this is to look at the shape of the ion s LUMO (the LUMO is a molecule s electron acceptor orbital) Allyl cation s LUMO appears as four surfaces Two surfaces are positioned near each of the terminal carbon atoms and they identify allyl cation s electron acceptor sites... 

Criticize or defend the following proposition In dilute solutions, branching affects viscosity only inasmuch as the branched molecule has a more compact shape. At higher concentrations, the effect of branching is closer to a bulk effect. 

Equation (8.97) shows that the second virial coefficient is a measure of the excluded volume of the solute according to the model we have considered. From the assumption that solute molecules come into surface contact in defining the excluded volume, it is apparent that this concept is easier to apply to, say, compact protein molecules in which hydrogen bonding and disulfide bridges maintain the tertiary structure (see Sec. 1.4) than to random coils. We shall return to the latter presently, but for now let us consider the application of Eq. (8.97) to a globular protein. This is the objective of the following example. 

Adsorption Kinetics. In zeoHte adsorption processes the adsorbates migrate into the zeoHte crystals. First, transport must occur between crystals contained in a compact or peUet, and second, diffusion must occur within the crystals. Diffusion coefficients are measured by various methods, including the measurement of adsorption rates and the deterniination of jump times as derived from nmr results. Factors affecting kinetics and diffusion include channel geometry and dimensions molecular size, shape, and polarity zeoHte cation distribution and charge temperature adsorbate concentration impurity molecules and crystal-surface defects. 

Figure 2.1 Kendrew s model of the low-resolution structure of myoglobin shown in three different views. The sausage-shaped regions represent a helices, which are arranged in a seemingly Irregular manner to form a compact globular molecule. (Courtesy of J.C. Kendrew.)...

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