Molecular structures notation

RAMSES is usually generated from molecular structures in a VB representation. The details of the connection table (localized charges, lone pairs, and bond orders) are kept within the model and are accessible for further processes. Bond orders are stored with the n-systems, while the number of free electrons is stored with the atoms. Upon modification oF a molecule (e.g., in systems dealing with reactions), the VB representation has to be generated in an adapted Form from the RAMSES notation. 

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... 

Operational definitions of molecular structure are needed to clarify experimental significance. In addition, some statistical notation is needed to clarify physical meaning. All statistical definitions hinge on the minimum of potential energy in a bound electronic state, which defines the equilibrium geometry or r,-intemuclear distance type. 

The displacement of a signal from the hypothetical position of maximum shielding is called its chemical shift, notated as S (delta) and measured in parts per million (ppm). As indicated on Fig. 12-4, the zero of the 6 scale is conventionally located at the signal produced by the H s of tetramethylsilane (TMS), (CHj)4 Si. This compound serves because its H-signal is usually isolated in the extreme upheld region. Clues to the structure of an unknown compound can be obtained by comparing the chemical shifts of its spectrum to the d values in such tabulations as Table 12-3. Some generalizations about molecular structure and proton chemical shift in H nmr (pmr) arc ... 

SMILES (Simplified Molecular Input Line Entry Systems) is a line notation system based on principles of molecular graph theory for entering and representing molecules and reactions in computer (10-13). It uses a set of simple specification rules to derive a SMILES string for a given molecular structure (or more precisely, a molecular graph). A simplified set of rules is as follows ... 

Further information on notation is oontained in O, Himne s Molecular spectra and molecular structure, vol. II. Van Noatnmd Reinhold. 

The Simplified Molecular Input Line Entry System (SMILES) is frequently used for computer-aided evaluation of molecular structures [1-3]. SMILES is widely accepted and computationally efficient because SMILES uses atomic symbols and a set of intuitive rules. Before presenting examples, the basic rules needed to enter molecular structures as SMILES notation are given. 

To obtain a unique SMILES notation, computer programs such as the Toolkit include the CANGEN algorithm [1] which performs CANonicalization, resulting in unique enumeration of atoms, and then GENerates the unique SMILES notation for the canonical structure. In the case of pyridine, this is notation (III). Any molecular structure entered in the Toolkit is converted automatically into its unique representation. 

Fig. 11.8 Two 1-bromonaphthalene molecules in the layered clathrate isostructural with the one depicted in Fig. 11.2. The two non-related by crystal symmetry molecules as obtained by structure refinement and the respective orientational disordering modes which produce apparent molecular deformations (Notations as in Fig. 11.3)...

In order to calculate a physicochemical property, the structure of a molecule must be entered in some manner into an algorithm. Chemical structure notations for input of molecules into calculation software are described in Chapter 2, Section VII and may be considered as either being a 2D string, a 2D representation of the structure, or (very occasionally) a 3D representation of the structure. Of this variety of methods, the simplicity and elegance of the 2D linear molecular representation known as the Simplified Molecular Line Entry System (SMILES) stands out. Many of the packages that calculate physicochemical descriptors use the SMILES chemical notation system, or some variant of it, as the means of structure input. The use of SMILES is well described in Chapter 2, Section VII.B, and by Weininger (1988). There is also an excellent tutorial on the use of SMILES at www.daylight.com/dayhtml/smiles/smiles-intro.html. 

The molecular structure of phosphetane (6) was elucidated by X-ray crystallographic analysis, as discussed in Section II.89 The preferred isomer is (6-(l 4) (2 6)), which is shown in two space orientations in order to illustrate the application of the Permutational Notation. The ligand indices are prescribed by the Sequence Rules.75 The ligand and skeletal indices must coincide in (6-E), which thus gives the orientation of the skeleton. The permutation (1 4) (2 5) gives isomer (6 -(l 4) (2 5)) as a... 

It is clear that the entire electronic density in a molecule has the role of determining the nuclear distribution hence bonding, consequently, chemical bonding cannot be confined to lines in space. It is well understood that bond diagrams represent only an oversimplified, "short-hand" notation for the actual molecular structure, nevertheless, as most successful notations do, chemical bonds as formal lines have acquired an almost unquestioned reputation of their own as if they were truly responsible for holding molecules together. 

Figure 19. Molecular structures of the hydrogen-bridge diastereomers (a) (R,S)-(a a)-[p-N2H2 Fe(PPr3)(tpS4) 2] 2 THF and (b) (R,S)-(P P)-[p-N2H2 Fe(PPr3)(tpS4) 2] 4 CH2C12 [The notation (a a) and (P P) corresponds with the notation introduced in Section IV.D for the thiolate atoms involved in bridges.]...

In this section, actual molecular structures are shown for the various point groups. The Schoenflies notation is used and the characteristic symmetry elements are enumerated. 

To avoid any misinterpretations concerned with the digit style of numbers, the decimal point is used throughout the book instead of a comma (i.e. computer notation 1.03 instead of 1,03, except for some graphical representations). In representative molecular structures, spin-paired non-bonding electrons around an atom of a molecule are represented (if necessary) by a bold line —in accord with commonly used leivis-structures. Single electrons are represented by a dot A full arrow (-> ) indicates shifts of electron pairs, whereas single electron shifts are... 

Notation Systems. Specific aspects of significance may be recorded independently within a unique code representation, as is done by several codes for molecular structure. Thus searching operations may be directed to the total compound, to various substituent groups, or to individual symbols or combinations... 

Figures 5.7 and 5.8 sketch a picture of the first two permanent electric moments (au) for a selection of noncentrosymmetric and centrosymmetric molecules, respectively. The notation is the same as that given in Mag-nasco et al. (1988). It is understood that the point-like multipoles are placed at the centre of mass of the molecule, their sign in relation to the molecular structure of the monomer being of fundamental importance in determining the nature of the electrostatic interaction (attractive or repulsive). The numbers shown in each figure are from SCF calculations and so are little larger than those given in Table 5.2.

Atom indices describe atoms of a molecule, based on their neighborhood as well as their electronic and physical properties. The notation topologicar clearly indicates that such an index includes information about the molecular structure - and is thus more than a simple atom parameter. Commonly used indices are topological state indices and electrotopological state indices. 

The investigation of molecular structures and their properties is one of most fascinating topics in chemistry. Since the first alchemy experiments, scientists have created a language consisting of symbols, terms, and notations to describe compounds, molecules, and their properties. This language was refined to give a unique notation known today by scientists all over the world. The increasing use of computational... 

Most methods to determine molecular structures try to compensate for or correct the effect of the vibration-rotation terms. As a result, there are now multitudes of methods available with as many special notations as methods. Their isotope dependence varies in practice from zero to full (for vq structures). Their error limits are sometimes difficult to determine. The goals of some of the newer methods are internal consistency and maximum relative errors (difference to Vg structure) of 0.1% or less. 

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