Groups of atoms

Strictly speaking, a group of atoms cannot be isolated from the rest of the molecule. However, with a few exceptions, the same group always... 

Many surfaces have additional defects other than steps, however, some of which are illustrated in figure A1.7.1(b). For example, steps are usually not flat, i.e. they do not lie along a single low-mdex direction, but instead have kinks. Terraces are also not always perfectly flat, and often contain defects such as adatoms or vacancies. An adatom, is an isolated atom adsorbed on top of a terrace, while a vacancy is an atom or group of atoms missing from an otiierwise perfect terrace. In addition, a group of atoms called an island may fonn on a terrace, as illustrated. 

Covalent bonding, in all the cases so far quoted, produces molecules not ions, and enables us to explain the inability of the compounds formed to conduct electricity. Covalently bonded groups of atoms can, however, also be ions. When ammonia and hydrogen chloride are brought together in the gaseous state proton transfer occurs as follows ... 

Besides specifications on atoms, bonds, branches, and ring closure, SLN additionally provides information on attributes of atoms and bonds, such as charge or stereochemistry. These are also indicated in square [ ] or angle < > brackets behind the entity e.g., trans-butane CH3CH=[s=t]CHCH3). Furthermore, macro atoms allow the shorthand specification of groups of atoms such as amino adds, e.g., Ala, Protein2, etc. A detailed description of these specifications and also specifications for 2D substructure queries or combinatorial libraries can be found in the literature [26]. 

Three record types are used to group other records TER indicates the end of a chain, while MODEL/ENDMDL surround groups of ATOM, HETATM. TER and similar records. 

If S is a single atom or a group of atoms with the bonds attached to the same atom (such as a CHi group), then we have the additivity of bond properties, liie first-order approximation, as given by Eq. (3). 

The course of aromatic substitution has been placed on a more scientific basis by the following rules of Hammick and Illingworth (jfour. Chem. Soc., 930. 2358), If a monosubstituted benzene derivative has the formula CgHsXY, where X is the atom joined to the benzene ring and Y is an atom or group of atoms attached to X, then —... 

Polyatomic molecules vibrate in a very complicated way, but, expressed in temis of their normal coordinates, atoms or groups of atoms vibrate sinusoidally in phase, with the same frequency. Each mode of motion functions as an independent hamionic oscillator and, provided certain selection rules are satisfied, contributes a band to the vibrational spectr um. There will be at least as many bands as there are degrees of freedom, but the frequencies of the normal coordinates will dominate the vibrational spectrum for simple molecules. An example is water, which has a pair of infrared absorption maxima centered at about 3780 cm and a single peak at about 1580 cm (nist webbook). 

The solvent accessible surface area (SASA) method is built around the assumption that the greatest amount of interaction with the solvent is in the area very close to the solute molecule. This is accounted for by determining a surface area for each atom or group of atoms that is in contact with the solvent. The free energy of solvation AG° is then computed by... 

Molecular vibrations are the basis of infrared (IR) spectroscopy Certain groups of atoms vibrate at characteristic frequencies and these frequencies can be used to detect the pres ence of these groups in a molecule... 

Functional group (Section 4 1) An atom or a group of atoms in a molecule responsible for its reactivity under a given set of conditions... 

To limit a semi-empirical calculation to part of a molecule, select the atoms of interest. Then choose Bttend to sp3 on the Select menu to terminate correctly the selected group of atoms. Only the selected atoms move, but the frozen atoms influence the calculation. This is now possible with all the semi-empirical methods in HyperChem. 

Substitution means the replacement of one or more hydrogen atoms in a given compound by some other kind of atom or group of atoms, functional or nonfunctional. In substitutive nomenclature, each substituent is cited as either a prefix or a suffix to the name of the parent (or substituting radical) to which it is attached the latter is denoted the parent compound (or parent group if a radical). 

When it is required to indicate the number of entire groups of atoms, the multiplicative numerals bis-, tris-, tetrakis-, pentakis-, and so on, are used (i.e., -kis is added starting from tetra-). The entity to which they refer is placed in parentheses. 

Conservation of mass also can, with care, be applied to groups of atoms. For example, the ammonium ion, NH4, can be precipitated as Fe(NH4)2(S04)2 6H2O. Selecting NH4 as the reaction unit gives... 

Rearrangement ion. An electrically charged dissociation product, of a molecular or parent ion, in which atoms or groups of atoms have transferred from one portion of the molecule or molecular moiety to another during the fragmentation process. 

Other general circumstances in which normal vibrations tend to be localized in a particular group of atoms arise when there is a chain of atoms in which the force constant between two of them is very different from those between other atoms in the chain. For example, in the molecule HC=C—CH=CH2 the force constants in the C—C, C=C and C=C bonds are quite dissimilar. It follows that the stretchings of the bonds are not strongly coupled and that each stretching vibration wavenumber is typical of the C—C, C=C or C=C group. 

The word ligand to describe an atom, or group of atoms, attached to a central metal atom can also be confusing. This has arisen because the type of bonding in complexes tends to be different from that in, say, H2O. However, the difference is quantitative rather than... 

In the examples, a nitro group is substituted for a hydrogen atom, and water is a by-product. Nitro groups may, however, be substituted for other atoms or groups of atoms. In Victor Meyer reactions which use silver nitrite, the nitro group replaces a hahde atom, eg, I or Br. In a modification of this method, sodium nitrite dissolved in dimethyl formamide or other suitable solvent is used instead of silver nitrite (1). Nitro compounds can also be produced by addition reactions, eg, the reaction of nitric acid or nitrogen dioxide with unsaturated compounds such as olefins or acetylenes. 

Step 12. FinaHy, the crystaHographer analy2es the results, tabulates some critical information (eg, bond distances, bond angles, torsion angles, planarity of groups of atoms, etc), and prepares a report on the stmcture deterrnination. The time for stmcture solution and refinement as outlined here is normally 2 to 8 h depending on the complexity of the stmcture. 

These stmctures tend to have a lot of disorder. It is rare that any hydrogens can be observed in the final electron density maps. In fact, many groups of atoms (water molecules and some side chains) may be so disordered that it is usually difficult to determine positions for these groups. 

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