Molecular representation

Figure 8.9 TbPc2-based single ion magnets (SIMs) [90] (a) Schematic representation molecular localization of the three spin-systems characteristics of the [TbPc2]° complex J = 6, the uniaxial magnetic moment of the 4f configuration / = 3/2 nuclear spin of the only stable and naturally occurring 159Tb isotope S = 1/2 organic radical delocalized over the two Pc ligands. The radical...

Commonly used molecular descriptor types are listed. For each category, one or two representative examples are given. Dimensionality refers to the molecular representation (molecular formula, 2D drawing, or 3D conformation) from which the descriptors are calculated (adapted from ref. 4). 

In this chapter, we will give a brief introduction to the basic concepts of chemoinformatics and their relevance to chemical library design. In Section 2, we will describe chemical representation, molecular data, and molecular data mining in computer we will introduce some of the chemoinformatics concepts such as molecular descriptors, chemical space, dimension reduction, similarity and diversity and we will review the most useful methods and applications of chemoinformatics, the quantitative structure-activity relationship (QSAR), the quantitative structure-property relationship (QSPR), multiobjective optimization, and virtual screening. In Section 3, we will outline some of the elements of library design and connect chemoinformatics tools, such as molecular similarity, molecular diversity, and multiple objective optimizations, with designing optimal libraries. Finally, we will put library design into perspective in Section 4. 

Valence-bond representation Molecular-orbital representation it bonding and multicenter it bonds Shapes of molecules Coordination compounds Isomerism Bonding in metals... 

Some representive molecular structures are given in Figs. 3 to 5. 

In this chapter we shall combine some of the ideas described in Chapters 3 and 4 the applications of topological concepts and methods for the study of various representations of molecular shapes. Among the shape representations molecular contour surfaces have a prominent role, but we shall also consider alternatives, primarily for the purposes of characterizing the large scale shape features of biological macromolecules. 

Fig. 2. 2D representation (molecular graph) of icosahedral Qo, with faces labelled according to an orange peel scheme. The pentagonal face labelled 32 lies on the opposite side of the molecule to the pentagonal face labelled 1. 

The two-dimensional representation of a molecule considers how the atoms are connected, i.e. it defines the connectivity of atoms in the molecule in terms of the presence and nature of chemical bonds. Approaches based on the -+ molecular graph allow a two-dimensional representation of a molecule, usually known as the topological representation. Molecular descriptors derived from the algorithms applied to a topological representation are called 2D-descriptors, i.e. they are the so-called - graph invariants. 

D (two-dimensional) descriptors derived from algorithms applied to a topological representation (molecular graph). 

Chemists have historically employed various means of representating molecular structure. Two-dimensional drawings of atoms connected by lines are some of the most common molecular representations. Each line represents a chemical bond that, in the simplest case, is a pair of electrons shared between the connected atoms, resulting in a very strong attractive interatomic force. The various interatomic forces define the structure or shape of a molecule, while its chemistry is dependent on the distribution of electrons. A chemical reaction involves a change in the electron distribution, i.e., a change in bonding. 

Extended Connection Table Representation molecular graph... 

Quantum Self-Similarity Measures quantum similarity quantum similarity = quantum similarity Quantum Similarity Indices quantum similarity Quantum Similarity Measures quantum similarity representation molecular descriptors rigidity —> flexibility indices... 

The ultimate goal of a thermodynamic description of molecular systems, however, is to determine the horizontal displacements of the electronic structure (see Section 7), i.e., transitions from one v-representable molecular density to another. In order to relate the information entropy H[p], possibly involving also the reference densities (equation (92)), to the system energetic parameters one uses the generalized variational principle in the entropy representation [108] ... 

Compound Name Molecular Representation Molecular Formula... 

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