The Homology Relation between Molecules: a Revival of an Old Way for Classification of Molecules

The homology (homolo) relation between molecules was introduced. This relation is a generalization of an old idea of series of homologous compounds. The homolo relation operates on a molecule by removing all the structural fragments that are identical with a certain selected fragment. As a result a multiset of fragments is produced. It was shown that the homolo relation is an equivalence relation in a set of molecules. Thus, by choosing various reference fragments, the molecules can be classified in many different ways. Using the language of homolo operation it is possible to redefine such ideas as constitutional and stereo isomers as well as a generator of a molecule and, for instance, factorization of a molecule onto fragments. </p

Classification of Topological Isomers: Knots, Links, Rotaxanes, etc.

Topological isomers, i.e., knots, catenanes, rotaxanes, pseudoknots, hook-and-ladder, and Möbius molecules have so far been left out from the isomer classification schemes discussed. To expand the classification schemes to include the topological molecules such as knots and links, questions about the number of components and the number of crossings are incorporated into the scheme. In the case of rotaxanes and pseudoknots, which are topologically trivial, a procedure making them not trivial is described. For the hook-and-ladder as the well as Möbius type of isomers, a procedure is given that allows their classification. All the new procedures are included into the new classification scheme in such a way that all questions about topology precede the ordinary question tree. In that way, a molecule is first classified as a topological object, and then classical questions about its structure are asked

HCNCC -the possible isomer of cyanoacetylene

Abstract HCNCC, the exotic linear rearrangement of cyanoacetylene, is a probable interstellar molecule. The Letter compares CCSD(T)/aug-cc-pVTZ energies of five cyanoacetylene isomers, and predicts properties of the HCNCC ground singlet electronic state: geometry, equilibrium rotational constant, electric dipole moment and vibrational frequencies -based on the coupled-clusters and density functional theory (B3LYP/aug-cc-pVTZ) studies

The Homology Relation between Molecules: a Revival of an Old Way for Classification of Molecules

The homology (homolo) relation between molecules was introduced. This relation is a generalization of an old idea of series of homologous compounds. The homolo relation operates on a molecule by removing all the structural fragments that are identical with a certain selected fragment. As a result a multiset of fragments is produced. It was shown that the homolo relation is an equivalence relation in a set of molecules. Thus, by choosing various reference fragments, the molecules can be classified in many different ways. Using the language of homolo operation it is possible to redefine such ideas as constitutional and stereo isomers as well as a generator of a molecule and, for instance, factorization of a molecule onto fragments. </p

The Acid-Base Through-the-Cage Interaction as an Example of an Inversion in a Cage Isomerism

We define a new inversion in a cage isomerism (ic): X@C⋯Y₪icY@C⋯X, (₪ is the isomerism relation) as an isomerism in the three-component system of molecules X, Y, and a cage C, in which one of the molecules is located inside and the other outside the cage. The ic isomerism is similar to the endo-exo one, which occurs only if either the interior or exterior of C is empty. By contrast, ic occurs only if neither the interior nor the exterior of C is empty. We also discuss the other closely related types of isomerisms are also discussed. Calculations of the XH⋯NH3@C60 and NH3⋯HX@C60ic isomers were performed at the &omega;B97XD/Def2TZVP level. The calculated energies demonstrated that the systems with the HX acid outside (X = F, Cl) and the NH3 base inside the cage, XH⋯NH3@C60, are more stable than their ic isomers, NH3⋯HX@C60, by about 4&ndash;8 kcal/mol. This is because NH3 is more stabilized inside the cage than HX (a matter of 6.5 kcal/mol). In the studied systems and subsystems, the HX molecules are Lewis acids and the NH3 molecule is always a Lewis base. The C60 molecule with HX inside or outside the cage is also an acid for the NH3 base positioned outside or inside the cage. On the other hand, the C60 cage is truly amphoteric because it is simultaneously an acid and a base

Heteroatom Incorporation Effect in σ- and π-Electron Systems: The sEDA(II) and pEDA(II) Descriptors

The effect of heteroatom or heteroatomic group incorporation into unsaturated five- and six-membered cyclic systems was studied by means of DFT/B3LYP/aug-cc-pVDZ calculations. Two descriptors of the incorporation effect, sEDA­(II) and pEDA­(II), reflecting the influence of the incorporated atom or group on the population of the σ and π valence electrons, were constructed on the basis of natural bond orbital analysis. The sEDA­(II) and pEDA­(II) descriptors were shown to be linearly independent; the former correlated very well with electronegativity scales, whereas the latter correlated with NICS(1)_ZZ and HOMA_CC aromaticity indices. The two descriptors seem to be universal tools for analyzing different chemical and physicochemical effects occurring in unsaturated heterocyclic systems