Describing Molecules

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 

Let us start with a basic definition of a molecnlar descriptor  

A molecular descriptor represents a certain property or a set of properties of a 

Let ns stay a bit with the example of the spectroscopist. Let ns assume he is a specialist in infrared spectroscopy. One of the features of a structural drawing he wonld pay special attention to is hydroxy groups. The reason he does this is because his experience tells him that hydroxyl groups can usually be seen as a broad band at the beginning of an infrared spectrum. He translates this information almost automatically into a hydroxyl band in the spectrum. 

In fact, the infrared spectrnm is nothing else than a molecular descriptor that represents a certain property of the molecule its vibrational behavior under infrared radiation. If we look from this standpoint at molecular descriptors, several well-known strnctnral descriptors are already used in the day-to-day laboratory of a scientist. 

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The concept of corresponding states was based on kinetic molecular theory, which describes molecules as discrete, rapidly moving particles that together constitute a fluid or soHd. Therefore, the theory of corresponding states was a macroscopic concept based on empirical observations. In 1939, the theory of corresponding states was derived from an inverse sixth power molecular potential model (74). Four basic assumptions were made (/) classical statistical mechanics apply, (2) the molecules must be spherical either by actual shape or by virtue of rapid and free rotation, (3) the intramolecular vibrations are considered identical for molecules in either the gas or Hquid phases, and (4) the potential energy of a coUection of molecules is a function of only the various intermolecular distances. 

In Chapter 1, we introduced one of the best ways of drawing molecules, bond-line structures. They are fast to draw and easy to read, but they have one major deficiency they do not describe molecules perfectly. In fact, no drawing method can completely describe a molecule using only a single drawing. Here is the problem. 

Chemists use both chemical names and molecular pictures to describe molecules. Molecular pictures take several forms, including structural formulas, ball-and-stick models, space-filling models, and line structures. These molecular representations can help you improve your ability to think molecules. ... 

Graphs have been applied in chemometrics to describe molecules. Indeed, molecules can be represented as nodes (the atoms) connected by bonds (the edges). Because in the present chapter, we want to emphasize the optimization aspect, we refer the reader to the literature e.g. Refs. [20-23]. 

The VB and the MO methods are rooted in very different philosophies of describing molecules. Although at the outset each method leads to different approximate wave functions, when successive improvements are made the two ultimately converge to the same wave function. In both the VB and MO methods, an approximate molecular wave function is obtained by combining appropriate hydrogen-like orbitals on each of the atoms in the molecule. This is called the linear combination of atomic orbitals (LCAO) approximation. 

These papers describe molecules with LLPCN > 6. 

Resonance structures are useful because they allow us to describe molecules, radicals, and ions for which a single Lewis structure is inadequate. 

One of the most important factors when describing molecules that have only single bonds is the repulsion that exists between electrons. Repulsion is related to the number of electron pairs both shared and unshared around the central atom. When only two pairs of electrons surround the central atom (as in BeH2), the structure is almost always linear because that gives the configuration of lowest energy. 

The prospect of elucidating the course and mechanism of chemical reactions by some procedure such as RG looks rather bleak. What has been suggested [132] is that RG could be used to identify an effective interaction to describe molecules at the bond level and replace ab initio computations that start at the individual electron level. However, the formal resemblance of chemical reactions to phase transitions may clarify some properties of the former. 

A special class ofblock copolymers with blocks of very different polarity is known as amphiphilic (Figure 10.1). In general, the word amphiphile is used to describe molecules that stabilize the oil-water interface (e.g., surfactants). To a certain extent, amphiphilic block copolymers allow the generalization of amphi-philicity. This means that molecules can be designed that stabilize not only the oil-water interface but any interface between different materials with different cohesion energies or surface tensions (e.g., water-gas, oil-gas, polymer-metal, or polymer-polymerinterfaces). This approach is straightforward, since the wide variability of the chemical structure of polymers allows fine and specific adjustment of both polymer parts to any particular stabilization problem. 

In 1891, Fischer proposed 28> describing molecules with asymmetric C-atoms with their two-dimensional projections. This projection is illustrated with the example of D-glyceraldehyde 23. 

The reference 4 authors discuss criteria that should be applied when describing molecules with these molecular mechanics programs. Some of these are as follows (1) Check the error file for interactions not in the parameter set, because some programs will assign a force constant of zero to unrecognized atom types (2) check all interactions generating >5 kJ/mol of strain to determine, for instance, whether that bond or angle really is that strained or whether there is a parameterization or molecular structure problem and (3) check the... 

Schonflies notation is widely used to describe molecules or assemblages of atoms (polyhedron) such as the local environment of an atom. Thus, it is widely used to describe the symmetry of structural sites. It is a more compact notation but less complete than the Hermann-Mauguin notation. It consists generally of one capital letter, followed by one subscript number and one final letter. 

Cubic symmetry T for 4 axes (tetrahedral), O for 8 axes (octahedral) and I for 20 axes (icosahedra, exists to describe molecules but not crystals) ... 

Quantum mechanics describes molecules in terms of interactions among nuclei and electrons, and molecular geometry in terms of minimum energy arrangements of nuclei. All quantum mechanical methods ultimately trace back to the Schrodinger equation, which for the special case of hydrogen atom (a single particle in three dimensions) may be solved exactly. ... 

To a synthetic chemist the concept of a polymer is rather different. The term is often used to describe molecules formed from quite small numbers of monomers units but which resist crystallization and purification owing to the range of chain lengths present. Such materials will normally form brittle solids which are either amorphous or have a low level of crystalline order. 

Alkanes A family of saturated hydrocarbons with the general formula C H2n+2. The term saturated, in this context, is used to describe molecules that have only single bonds. The alkanes can only undergo substitution reactions in which there is replacement of one atom in the molecule by another atom. 

Alkenes A family of unsaturated hydrocarbons with the general formula CnH2n. The term unsaturated, in this context, is used to describe molecules which contain one or more carbon-carbon double bonds. Unsaturated compounds undergo addition reactions across the carbon-carbon double bonds and so produce saturated compounds. The addition of hydrogen across the carbon-carbon double bonds is used to reduce the amount of unsaturation during the production of margarines. 

As an alternative to describing molecules by their structural features (substruc-tural elements, functional groups) and similarly to CoMFA, this approach uses field points to describe the van der Waals and electrostatic minima and maxima that surround molecules and compares these field points. The field points that are used are derived from molecular electrostatic potential descriptors. The XED model is marketed by Cresset Biomolecular and forms the basis for the proprietary virtual screening technology FieldPrint [95]. 

Define and describe molecules, atoms, compounds, mixtures. 

What term describes molecules without a plane of symmetry ... 

Use the word atoms when describing a single element use the word molecules when describing molecules and compounds. 

It is possible to go beyond the dipole approximation in the length gauge and treat the interactions between higher multipoles with the field derivatives, which is relevant when the variation of the field with ry- cannot be neglected [3], However, we do not pursue these extensions here because, in all the applications discussed below, the dipole approximation will be found to suffice. Equations (1.50), (1.51), and (1.52) are the central expressions used below to describe molecule-light interactions. Extensions of this approach to include quantization of the electromagnetic field are described in Chapter 12. 

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