Atoms and bonds in molecules and chemical explanations

The concepts of atoms and bonds in molecules which appeared in chemistry during the nineteenth century are unavoidable to explain the structure and the reactivity of the matter at a chemical level of understanding. Although they can be criticized from a strict reductionist point of view, because neither atoms nor bonds are observable in the sense of quantum mechanics, the topological and statistical interpretative approaches of quantum chemistry (quantum theory of atoms in molecules, electron localization function and maximum probability domain) provide consistent definitions which accommodate chemistry and quantum mechanics.     

Atoms and bonds in molecules from radial densities

Radial densities are explored as an alternative method for partitioning the molecular density into atomic regions and bonding regions. The radial densities for atoms in molecules are similar to those of an isolated atom. The method may also provide an alternative to Bragg-Slater radii.     

Fourier analysis of the Compton profile: Atoms and molecules

Recent work has shown that the one-dimensional projection of the electron momentum density, the Compton profile, can be usefully interpreted as a position space quantity. This has led to an examination of B(r), the Fourier transform of the momentum density. A number of theoretical results relating to this new observable are given. The wave-mechanical representation with (natural) orbitals is employed, and this forms the basis for the subsequent analysis of B(r). The relationship of B(r) to overlap integrals and more generally to other electron density functions is considered. Atomic wavefunctions for krypton are used to illustrate the potential of this new approach to the analysis of momentum density data. General expressions are derived for atoms and molecules, and the radial and angular dependence of B(r) for various orbitals is displayed. The possibility of extracting accurate bond lengths from B(r) is assessed, and an example is given using some recent theoretical data for the fluorine molecule.     

Experimental electron density overlapping in hydrogen bonds: topology vs. energetics

We have investigated the relationship between the energetic properties of the hydrogen bond (HB) interaction and the topological overlapping of the electronic clouds at the HO critical point r_CP. This study involves a total of 83 X–HO (X=C, N, O) HBs, which have been described in terms of the topological properties of the electron density ρ(r) at r_CP for a large set of compounds. Kinetic G(r_CP) and potential V(r_CP) contributions to the local energy density of electrons exhibit linear functionalities against, respectively, the positive and negative curvatures of ρ(r) at the critical point, showing an effective deconvolution in the local form of the Virial theorem. The topological variation of the curvatures at r_CP, and therefore changes in the HO overlapping, are related to the onset of the repulsion between the electronic clouds of the basic and acid atoms.     

Transient bonds and chemical reactivity of molecules

Electron delocalization between the reagent and reactant molecules is the principal driving force of chemical reactions. It brings about the formation of new bonds and the cleavage of old bonds. By taking the aromatic substitution reaction as an example, we have shown the orbitals participating in electron delocalization. The interacting orbitals obtained are localized around the reaction sites, showing the chemical bonds that should be generated and broken transiently along the reaction path. By projecting a reference orbital function that has been chosen to specify the bond being formed on to the MOs of the reactant molecules, the reactive orbitals that are very similar to the interacting orbital have been obtained. The local potential of the reaction site for electron donation estimated for substituted benzene molecules by using these projected orbitals shows a fair correlation with the experimental scale of the electron-donating and -withdrawing strength of substituent groups. The reactivity is shown to be governed by local electronegativity and local chemical hardness and also by the localizability of interaction on the reaction site. © 1996 John Wiley & Sons, Inc.     

Atoms and molecules in cavities: A method for study of spatial confinement effects

A general method for solving the problems of spatially confined quantum mechanical systems is proposed. The method works within the framework of the model space approximation. In the case of atoms and molecules trapped into any-shape microscopic cavity (like molecular sieves or fullerenes), the method reduces to a simple modification of the commonly used basis-set quantum chemical calculations. The modification consists of a particular rotation and projection in the model space, leading to solutions better adapted to the boundary conditions of the spatial confinement than the functions that describe the free systems. To illustrate how this method works, it has been applied to the hydrogen atom confined in a spherical well, near a hard wall and confined in a cubic box. The results are also compared to the exact solutions. © 1995 John Wiley & Sons, Inc.     

Intramolecular halogen bonds in 1,2-aryldiyne molecules: a theoretical study

Intramolecular halogen bonds have been the subject of several current experimental and theoretical studies. In this work, intramolecular halogen bonds in a series of 1,2-aryldiyne molecules were investigated using density functional theory calculations at the M06-2x level of theory. For comparison, some dimeric complexes between halogenated aryldiynes and quinolinyl compounds were also considered. The calculated interatomic distances and interaction angles of intramolecular halogen bonds compare fairly well with those determined experimentally, and the triangle motifs retain almost perfectly planar in all the studied molecules. Many of the well-known properties of conventional halogen bonds are reproduced in intramolecular halogen bonds: the interaction strength tends to increase with the enlargement of the atomic radius of halogens (I > Br > Cl); the attachment of electron-withdrawing moieties to halogens leads to much stronger intramolecular halogen bonds; the X···N (quinolinyl) interactions are stronger than the X···O (carbonyl) halogen bonds. On the basis of the shorter interatomic distances and the larger values of electron densities at the bond critical points, intramolecular halogen bonds become stronger in strength than corresponding intermolecular halogen bonds. However, these interactions have similar structural, energetic, atoms in molecules (AIM), and noncovalent interaction index (NCI) characteristics to traditional halogen bonds. Therefore, these interactions can be recognized as halogen bonds that are primarily electrostatic in nature. Particularly, the formation of intramolecular halogen bonds gives rise to the essential coplanarity of the molecules, whereas the two subunits in the dimeric complexes deviate from planarity to a large degree. In addition, a small number of crystal structures containing intramolecular halogen bonds were retrieved from the Cambridge Structural Database (CSD), to provide more insights into these interactions in crystals. This work not only will extend the knowledge of noncovalent interactions involving halogens as electrophilic centers but also could be very useful in molecular design and synthetic chemistry.     

Charge fluctuations and correlation strength in chemical bonds: First-row homonuclear diatomic molecules

We investigate, by means of ab initio calculations, the strength of electron correlations within covalent bonds: the first-row homonuclear diatomics serve as test cases. As an appropriate measure of the correlation strength, we introduce the reduction of the mean-square deviations of the electronic charges in localized orbitals forming a bond. A recently developed population analysis in terms of local operators derived from localized molecular orbitals is thereby used. The correlation-strength parameter depends only weakly on dynamical correlations as test calculations demonstrate. Therefore, the full-valence complete active space self-consistent field (CASSCF) approximation is applied in order to study the changes in the correlation strength with changing bond length for different types of bonds. A number of simple rules emerge from this discussion. In addition, we show that charge fluctuations are not only a reliable measure of intrabond correlation effects, but also can be used to monitor intraatomic quasi-degeneracy effects as well as the interdependence within multiple bonds. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 157–173, 1998     

Hybridization in methylenecyclopropane and related molecules having exocyclic double bonds

The hybridization in methylenecyolopropane, dimethylenecyclopropane, bisethanoallene, and related molecules containing double bonds externally attached to a cyclopropane ring is considered by applying the method of maximum overlap. The results show that the bond overlap of an exocyclic double bond is larger than the bond overlap of a normal C=C bond, and double bonds in allenes have even larger overlap than an exocyclic C=C bond. The results of the calculations are correlated with some available experimental data.     

Criterion for estimate of NH bonds in porphyrin molecules

A group of criteria for estimating the state of the NH bonds in the molecules of poprhyrin ligands was determined, including the spectral (¹H NMR), kinetic, and quantum-chemical criteria. The above criteria can be used to characterize the chemical activity of the bonds in the structural groups of porphyrins known by this time and predict the reactivity of these compounds in reactions involving the coordination center. The change in the electronic absorption spectra of porphyrins observed on the change of a weakly solvating solvent for the electron-donor solvent was shown to be unreliable criterion of the state of the NH bonds in these molecules.     

How van der Waals bonds orient molecules in zeolites

We show that weak bonds are responsible for the way a molecule is held in a zeolite, and for its reactivity.     

Intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides: an atoms in molecules study

The molecular structure and relative stability of different conformers of isolated canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (pdT), 2-deoxycytidine-5'-phosphate (pdC), 2-deoxyadenosine-5'-phosphate (pdA), and 2'-deoxyguanosine-5'-phosphate (pdG) were calculated using the B3LYP/6-31++G(d,p) level of theory. The results of the calculations reveal that, for all nucleotides except pdG, conformers with a syn orientation of the base do not correspond to a minimum on the potential energy surface. In the case of pdA and pdC, conformers with an orthogonal orientation of the nucleobase are located instead, north/syn conformers. These conformers as well as syn conformers of pdG are stabilized by intramolecular N-H...O hydrogen bonds. Analysis of the electron density distribution within the atoms in molecules theory reveals the presence of numerous C-H...O hydrogen bonds in the nucleotides. However, a more detailed consideration of the properties of these bonds demonstrates that many of them should be considered as strong attractive electrostatic interactions rather than true hydrogen bonds. True hydrogen bonds are represented mainly by C6/ C8-H...O5'/O-P in anti conformers and the N-H...O-P bonds in syn conformers. It is demonstrated that the values of ellipticity of the electron density at the bond critical point (BCP) and the distance between BCP and ring critical point are the most reliable indicators for determining the true intramolecular hydrogen bonds.     

Photophysical processes and the photodissociation of chemical bonds in polyatomic molecules

The main concepts of the nature of electronically excited states in polyatomic molecules and the intramolecular and intermolecular processes of their evolution are reported. The dependence of the probabilities of these processes on the electronic structure of the molecule is considered. Possible mechanisms of the dissociation of electronically excited molecules with bond cleavage are discussed, and the theoretical results of this consideration are given. The experimental data obtained by the authors are interpreted. In this case, attention is focused on C-H-bond photodissociation processes in a condensed phase, which are the best studied processes. The dissociation of other bonds is briefly discussed.