Polarization, atomic

There is a pronounced tendency for boron to become bonded to the less substituted car bon of the double bond Thus the hydrogen atoms of diborane add to C 2 of 1 decene and boron to C 1 This is believed to be mainly a steric effect but the regioselectivity of addition does correspond to Markovmkov s rule m the sense that hydrogen is the neg atively polarized atom m a B—H bond and boron the positively polarized one... 

Unstable because of adjacent positively polarized atoms... 

Positively polarized atoms not adjacent most stable intermediate... 

The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neutralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and p sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

Dipole-dipole attraction (Section 2.17) A force of attraction between oppositely polarized atoms. 

Hydrogen bonds 12-30 0.3 Relative strength is proportional to the polarity of the H bond donor and H bond acceptor. More polar atoms form stronger H bonds. 

The electrophilic sink must be able to accept an electron pair, usually because it has either a positively charged atom or a positively polarized atom in a functional group, for example ... 

Cartesian and cylindrical polar atomic coordinates of the structural repeating unit of 31 polysaccharide helices are provided in Tables A1 to A31. Errors, if any, in the original publications have been corrected. The coordinates of hydrogen atoms are given in a majority of structures. If missing, they are not available in the references cited in Table I. Each table caption contains the structure number and polymer name assigned in Table I. Refer to Table II for its chemical repeating unit. Cartesian (x, y, z) and cylindrical (r, , z) coordinates are related by x r cost ), y = r sin<(> and z is the same in both systems. 

A number of explanations have been offered for the anomeric effect. The one ° that has received the most acceptance is that one of the lone pairs of the polar atom connected to the carbon (an oxygen atom in the case of 93)... 

Molecules with polar atoms or charged groups can form intramolecular interactions such as internal H-bonds or cation-rr interactions. As a consequence energy minimization in vacuo often results in electrostatically collapsed conformations due to the dominance of these intramolecular interactions. Several compounds in... 

MSMS16 to evaluate the surface area, with a surface area free energy for non-polar atoms taken from Sitkoff et al.14... 

Hydrogen bonding descriptors the counts of hydrogen bond acceptors (HAG) or donors (HDO) the number of polar atoms, Pjt [34] the polar surface area in (PSA) and normalized to the total surface area (%PSA) ... 

The differences can also be seen in Figure 15.4, which compares cumulative distributions of these properties between the Gasteiger and Roche datasets. Many of the literature compounds are very simple, with low molecular weight, few polar atoms, and few functional groups. They have often been included in solubility datasets because they are well characterized and because accurate solubility data are available for them, rather than because they are druglike. The inclusion of many such simple compounds in a training set for a solubility prediction tool may focus the tool on an area of chemistry space that is not well populated with druglike molecules and may make the tool less useful for the prediction of the solubility... 

The lipids are a large and heterogeneous group of substances of biological origin that are easily dissolved in organic solvents such as methanol, acetone, chloroform, and benzene. By contrast, they are either insoluble or only poorly soluble in water. Their low water solubility is due to a lack of polarizing atoms such as 0, N, S, and P (see p.6). 

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