Atoms and bonds

The idea that matter is composed of a very large number of extremely small particles that we cannot see is very old, and most likely stems from the simple observation that any piece of matter can be divided into smaller and smaller parts without any apparent limit to the number of times this operation can be carried out. Traditionally, Lucretius is credited with the first sketch of a theory on the existence and properties of atoms, literally, things that cannot be cut into smaller pieces, although what he and the Greek philosophers before him meant by an atom has not even the vaguest affinity with our present concept. 

Strange as it may seem, the key to progress towards a reliable atomic conception of matter was a very humble instrument, the balance. It was in fact through weight laws - Boyle and Lavoisier - that modern science arrived at a proper understanding of the atomic and molecular structure of matter. The discovery of the electron and quantum mechanics completed the job at the beginning of the last century. 

Recourse to the details of the electron distribution for the explanation of chemical phenomena is rigorous but sometimes awkward, and chemistry has always striven 

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Chemistry, like any scientific discipline, relies heavily on experimental observations, and therefore on data. Until a few years ago, the usual way to publish information on recent scientific developments was to release it in books or journals. In chemistry, the enormous increase in the number of compounds and the data concerning them resulted in increasingly ineffective data-handling, on the side of the producers as well as the users. One way out of this disaster is the electronic processing, by computer methods, of this huge amount of data available in chemistry. Compared with other scientific disciplines that only use text and numbers for data transfer, chemistry has an additional, special challenge molecules. The molecular species consist of atoms and bonds that hold them together. Moreover, compounds... 

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]. 

Figure 2-11. Phenylalanine can be represented in graph theory as a labeled, weighted graph with different atom and bond types (as on the left-hand side).

The matrix of a structure with n atoms consists of an array of n / u entries. A molecule with its different atoms and bond types can be represented in matrix form in different ways depending on wbat kind of entries are chosen for the atoms and bonds. Thus, a variety of matrices has been proposed adjacency, distance, incidence, bond, and bond-electron matrices. 

Central the molecular graph is completely coded (each atom and bond is represented) matrix algebra can be used the niimber of entries in the matrix grows with the square of the number of atoms in ) no stereochemistry included... 

The first line of the connection table, called the counts line (see Figure 2-21), specifies how many atoms constitute the molecule represented by this file, how many bonds arc within the molecule, whether this molecule is chiral (1 in the chiral flag entry) or not, etc. The last-but-onc entry (number of additional properties) is no longer supported and is always set to 999. The last entry specifics the version of the Ctab format used in the current file. In the ease analyzed it is V2000". There is also a newer V3000 format, called the Extended Connection Table, which uses a different syntax for describing atoms and bonds [50. Because it is still not widely used, it is not covered here. 

Atomic and bond hash codes are helpful in structure manipulation programs, e.g., in reaction prediction or in synthesis design [99]. 

The most important feature of editing software is the option to save the structure in standard file formats which contain information about the structure (e,g., Mol-filc. PDB-filc). Most of these file formats arc ASCII text files (which can be viewed in simple text editors) and cover international standardized and normalized specifications of the molecule, such as atom and bond types or connectivities (CT) (see Section 2,4). Thus, with these files, the structure can be exchanged between different programs. Furthermore, they can seiwe as input files to other chemical software, e.g, to calculate 3D structures or molecular properties. 

Ring perception and equivalence of atoms and bonds are also very important tasks in for processing chemical compounds. 

Reactions can be considered as composite systems containing reactant and product molecules, as well as reaction sites. The similarity of chemical structures is defined by generalized reaction types and by gross structural features. The similarity of reactions can be defined by physicochemical parameters of the atoms and bonds at the reaction site. These definitions provide criteria for searching reaction databases [23],... 

Physticochemical coiiatrainla Further constraints can be imposed on the atoms and bonds of the reaction center, such as those physicochemical factors calculated by the PETRA package (see Section 7.1). For example, the partial charges calculated by the PEOE method can be used to extract the chemically feasible reaction from the two conceivable ones as illustrated in Figure 10.3-11. 

Figure 10.3-16. Graphical representation of the chemical structure of the reactants and products of a chemical reaction a) as a 2D image b) with structure diagrams showing all atoms and bonds of the reactants and products to indicate how this information is stored in a connection table.

Figure 10.3-19. Representation of the reaction shown fn Figure 10.3-16, indicating all the atoms and bonds of the chemical structures as well as the reaction center. For the sake of clarity, the coenzyme A has been abbreviated.

All this information is now directly. searchable. All chemical species can be searched not only by name, but also by structure and substructure, and by their role in a reaction. Reactions can be searched by all the species involved but also by the types of atoms and bonds contained in the reaction center,... 

The tutorial in Section 10.3.1.8 presents some of the various ways the information in the Biochemical Pathways database can be retrieved. In this tutorial the importance of searching for the reaction center, the atoms and bonds directly involved in the bond rearrangement scheme, is emphasized, It is a prerequisite for getting a deeper understanding of chemical reactions. 

In a reaction, bonds are broken and made. In some cases free electrons are shifted also. The rcaciion center contains all the bond.s being broken or made during the reaction as well as all the electron rearrangement processes. The reaction uhstme-ture is the structural subunit of atoms and bonds around the reaction center that has to be present in a compound in order for the reaction to proceed in the foi"ward (synthesis) direction (Figure 10,3-32). Both characteristics of a reaction can be used to. search for reactions with an identical reaction center and reaction substructure but with different structural units beyond the reaction substructure. For example, this can be achieved by searching in a reaction database. 

Other techniques that work well on small computers are based on the molecules topology or indices from graph theory. These fields of mathematics classify and quantify systems of interconnected points, which correspond well to atoms and bonds between them. Indices can be defined to quantify whether the system is linear or has many cyclic groups or cross links. Properties can be empirically fitted to these indices. Topological and group theory indices are also combined with group additivity techniques or used as QSPR descriptors. 

With its flexible and logical search language, REACCS can retrieve molecular stmctures, the atoms and bonds that are transformed ia a reaction, relative and absolute stereochemistry, the role (reactant, product, solvent, or catalyst) of a molecule ia a reaction, reaction data (eg, temperature and yield), hterature references, and keyword descriptions of reaction types. 

Molecular Connectivity Indexes and Graph Theory. Perhaps the chief obstacle to developing a general theory for quantification of physical properties is not so much in the understanding of the underlying physical laws, but rather the inabiUty to solve the requisite equations. The plethora of assumptions and simplifications in the statistical mechanics and group contribution sections of this article provide examples of this. Computational procedures are simplified when the number of parameters used to describe the saUent features of a problem is reduced. Because many properties of molecules correlate well with stmctures, parameters have been developed which grossly quantify molecular stmctural characteristics. These parameters, or coimectivity indexes, are usually based on the numbers and orientations of atoms and bonds in the molecule. 

Compare and contrast the electrostatic potential map of a typical detergent with that of a typical soap (stearate). Which part of each molecule will be most water soluble (hydrophilic) Draw a Lewis structure that describes each molecule s water-soluble group (make sure you indicate all necessary formal charges and lone pairs). Which part(s) of each molecule will be most grease soluble (lipophilic) What kinds of atoms and bonds are found in these groups ... 

In the early days of chemical modelling, people did indeed construct models from plastic atoms and bonds, a mler and a pair of scissors. The tendency now is to reach for the PC, and one aim of this book is to give you an insight into the bewitching acronyms that lie behind the keystrokes and mouse clicks of a sophisticated modelling package. 

The atom and bond concepts dominate chemistry. Dalton postulated that atoms retained their identities even when in chemical combinations with other atoms. We know that their properties are sometimes transferable from one molecule to another for example, the incremental increase in the standard enthalpy of formation of a normal hydrocarbon per CHj group is —20.6 1.3 kJmol . We also know that more often there are subtle modifications to the electron density. 

In Chapter 3, we studied the topic of population analysis. In population analysis, we attempt a rough-and-ready numerical division of the electron density into atom and bond regions. In Mulliken theory, the bond contributions are divided up equally between the contributing atoms, giving the net charges. The aim of the present section is to answer the questions Are there atoms in Molecules , and if so, How can they be defined . According to Bader and coworkers (Bader, 1990) the answers to both questions are affirmative, and the boundaries of these atoms are determined by a particular property of the electron density. 

Auto Build This application has been built upon the knowledge and experiences of our working group in order that beginner has access to all pertinent information. Auto Build automatically adds in the sample query structure the appropriate atom and bond query features. Then clicking on SSS button initiates a substructure search. Some examples of the query features, which may be added to a query structure, are ... 

Finally, the atomic and bond indices can be combined to give indices for the whole unit. The zeroth-order connectivity indices and Oy for the entire molecule can be calculated as a summation over the vertices of the hydrogen suppressed graph, that is ... 

What does functional-group polarity mean with respect to chemical reactivity Because unlike charges attract, the fundamental characteristic of all polar organic reactions is that electron-rich sites react with electron-poor sites. Bonds are made when an electron-rich atom shares a pair of electrons with an electron-poor atom, and bonds are broken when one atom leaves with both electrons from the former bond. 

For a reaction to take place, reactant molecules must collide and reorganization of atoms and bonds roust occur. Let s again look at the addition reaction of HBr and ethylene, which takes place in two steps. 

As we have seen by comparing C02 and H20, the shape of a polyatomic molecule affects whether or not it is polar. The same is true of more complicated molecules. For instance, the atoms and bonds are the same in c/s-dichloroethene (28) and frans-dichloroethene (29) but, in the latter, the C—Cl bonds point in opposite directions and the dipoles (which point along the C—Cl bonds) cancel. Thus, whereas c/s-dichloroethene is polar, traws-dichloroethene is nonpolar. Because dipole momenrs are directional, we can treat each bond dipole moment as a vector. The molecule as a whole will be nonpolar if the vector sum of the dipole moments of the bonds is zero. 

Although an exact search can be useful, in most cases it does not give any more information than can be obtained from the printed CA. Substructure searches (SSS) are far more important, because there is no other way to get this information. If we do a substructure search on 4 in Figure A.l, we not only get all the answers we would get in an exact search, but all substances that contain, anywhere within their structure, the arrangement of atoms and bonds shown in 4. For example, 5,6,7, and 8 would all be retrieved in this search, but 9 would not be. The SSS searches typically retrieve from tens to hundreds of times as many answers as exact searches of the same stracture. Furthermore, the scope can be widened by the use of variable nodes. For example, the symbol X means any halogen, the symbol M any metal, and the symbol G allows the user to specify his or her own variable at that point (e.g., G =C1 or NO2 or Ph). As with an exact search, each answer can be displayed as described above. 

Table IV. Comparison of stability and structure of Ain clusters between ab initio and parameterized interaction results with two- and three-body terms (2+3-b) as well as using only the two-body (2-b) interaction. Binding energies (Dc in eV) per atom, and bond distances (rg in ao) are given...

Atom and bond fragments Substructures (atom groups) Substructure environment Number of carbon atoms Number of rings (In polycyclic compounds) Molecular connectivity (extent of branching)... 

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