Topological Analysis Of Charge Density Research Articles

Characterization of Bonding in Cesium Uranyl Chloride: Topological Analysis of the Experimental Charge Density

The topological analysis of the charge density distribution in Cs(2)UO(2)Cl(4) obtained from an accurate X-ray diffraction experiment at 20K is reported. Details of the techniques applied during data collection and data refinement are discussed. A split Hansen-Coppens multipole model for uranium and cesium atoms has been used to describe the charge density features associated with valence electrons and core deformations. The analysis of the deformation density distribution, QTAIM space partitioning, the Laplacian of the electron density, and electron localization function are discussed. Local QTAIM descriptors for bonds to uranium and cesium are reported, as well as integrated properties of each individual atom. U(5f), U(6s), U(6p), U(6d), and U(7s) shells were required to describe the aspherical charge density of the uranium pseudoatom. Observed deformation of the cesium atom core was described by applying the multipole model to Cs(5s) and Cs(5p) shells.

Topological analysis of charge densities obtained from experiment and plane-wave calculations

Topological analysis of charge densities obtained from experiment and plane-wave calculations

Charge Density Analysis of a Pentaborate Ion in an Ammonium Borate: Toward the Understanding of Topological Features in Borate Minerals

Structural and charge density distribution studies have been carried out on a single crystal data of an ammonium borate, [C(10)H(26)N(4)][B(5)O(6)(OH)(4)](2), synthesized by solvothermal method. Further, the experimentally observed geometry is used for the theoretical charge density calculations using the B3LYP/6-31G** level of theory, and the results are compared with the experimental values. Topological analysis of charge density based on the Atoms in Molecules approach for B-O bonds exhibit mixed covalent/ionic character. Detailed analysis of the hydrogen bonds in the crystal structure in the ammonium borate provides insights into the understanding of the reaction pathways that could result in the formation of borate minerals. The net atomic charges and electrostatic potential isosurfaces also give additional input to evaluate chemical and physical properties in such systems.

ChemInform Abstract: Electronic Structure and Conformational Properties of Vinylphosphonic Acid and Some Related Derivatives

The electronic structure and conformational properties of vinylphosphonic acid, vinylphosphoryl dichloride, and vinylphosphine oxide have been studied by ab initio quantum mechanical methods. Furthermore, the vinylphosphonic acid has been studied experimentally by means of 13 C NMR and ultraviolet spectroscopy. This compound has been synthesized by a modification of the McKenna hydrolysis reaction, improving significantly the yield. The ab initio calculations have been performed with different basis sets, including correlation energy at the MP2/6-31G * level. Topological analysis of charge density has also been carried out. Two conformers, s-cis and s-trans-gauche, have been determined for the internal rotation around the C-P bond, with low rotational barriers

Chemical bonding in the lightest tri-atomic clusters; H 3+, Li 3+ and B 3−

Detailed topological charge density analysis and the Quantum Theory of Atoms in Molecules (QTAIM) calculations has been performed on equilibrium geometries of the three lightest tri-atomic clusters; H 3 +, Li 3 + and B 3 −. Characteristics of critical points of charge density, the effects of occupied molecular orbitals on topology of charge density, the stability of molecular graphs toward nuclear excursions and the QTAIM integration results were used to draw a picture of bonding in these clusters. Topological networks in H 3 + and B 3 − are unstable but molecular graph of Li 3 + is stable under finite geometry changes. H 3 + is best represented as a 3-membered ring; lithium atoms in Li 3 + surround the electrons in basin of a Non-Nuclear Maximum (NNM) by an electrostatic interaction; and in B 3 − an extended bonding pattern was found.

A Computational Study on Some Viable Targets for Gas-Phase Synthesis of Metal Complexes of the Cyclic (B6C)−2and Their Bonding Pattern

In this account, a detailed computational study is conducted to verify the geometric, energetic, and electronic properties of the planar cyclic (B 6C) (-2) (as the simplest carrier of hexacoordinate carbon) within some metal complexes. The [M(B 6C)] ((-)) (M = Li, Na, K) and [M(B 6C)] (M = Be, Mg, Ca) series are employed for this purpose. Relevant ab initio calculations at both DFT and post-HF levels vividly demonstrate that this dianion is stabilized considerably in the electric field generated by cations, whereas the geometrical and electronic properties of this ring remain almost intact in these complexes. The complementary topological analysis of charge densities confirms that cyclic (B 6C) (-2) within these complexes exhibits the same topological patterns as the naked dianion, thus confirming the presence of an unusual charge density distribution in this dianion. An electrostatic model is proposed that not only qualitatively but also quantitatively explains the observed computational trends in these complexes. This model successfully traces the polarization of the central carbon atom of the ring in the presence of a hard, multiply charged cation. To facilitate experimental detection, the photoelectron spectra of the [M(B 6C)] ((-)) (M = Li, Na, K) series are computed and the dominant features are extracted. Although considered species are not global minima on their potential energy hypersurfaces, their kinetic stabilities are verified and demonstrated unequivocally.

Cyclopalladated Complexes of 3-Thiophosphorylbenzoic Acid Thioamides: Hybrid Pincer Ligands of a New Type. Synthesis, Catalytic Activity, and Photophysical Properties

Treatment of the 3-diphenylphosphorylbenzoic acid amides 3a,b with the Lawesson reagent resulted in 3-diphenylthiophosphorylbenzoic acid thioamides 4a,b, which easily underwent cyclopalladation at the C-2 position of the central benzene ring to give new hybrid pincer complexes 5a,b with κ3-SCS coordination. Molecular structures of the complexes were characterized by X-ray diffraction. The peculiarities of chemical bonding in 5a were investigated via topological analysis of charge density in the crystal. The palladium complexes 5a,b demonstrated high catalytic activity for the Suzuki cross-coupling reactions of aryl bromides with phenylboronic acid and exhibited luminescence at 77 and 300 K.

Ab initio post-HF study of electronic charge density distribution of cyclic (B 6C) −2: Concrete evidence of a novel bonding pattern

In this account, the bonding pattern of cyclic (B 6C) −2 dianion as a planar hypercoordinate carbon compound is considered employing topological charge density analysis developed within framework of Quantum Theory of Atoms in Molecules. The analysis was done on charge densities derived from post-HF methods. The outcomes of the analysis demonstrate that the nature of interactions between boron atoms and central carbon atom is a novel “non-directional shared interaction”. The intrinsic floppiness of charge density distribution in this molecule also is once again confirmed and a new approach is proposed to systematically study the role of nuclear excursions in similar molecules.

A new 4c–2e bond in B6H7−

For N(C(4)H(9))(4)B(6)H(7) a proton is shown to be localised above one of the faces of the distorted octahedron, and rhomboid rings are formed as shown by topological analysis of charge densities.

Ab initio charge density analysis of (B6C)2– and B4C3 species — How to describe the bonding pattern?

In this study, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM) developed by Bader and co-workers, has been accomplished (using the B3LYP method) on the CB62– anion and three planar isomers of the C3B4 species, which had been first proposed by Exner and Schleyer as examples of molecules containing hexacoordinate carbon atoms. The analysis uncovers the strong (covalent) interactions of boron atoms as well as the "nondirectional" interaction of central carbon atom with those peripheral atoms. On the other hand, instabilities have been found in the topological networks of (B6C)2– and B4C3(para) species. A detailed investigation of these instabilities demonstrates that the topology of charge density has a floppy nature near the equilibrium geometries of the species under study. Thus, these species seems to be best described as complexes of a relatively concrete ring containing boron or carbon atoms and a central carbon atom that is confined in the plane of the molecule, but with nondirectional interactions with the surrounding atoms.Key words: hypervalency, hexacoordinate carbon, quantum theory of atoms in molecules, charge density analysis, ab initio methods.

Topological analysis of charge densities in polymorphs of 3-acetylcoumarin

Topological analysis of charge densities in polymorphs of 3-acetylcoumarin

3,5-Dimethyl-1,3,5-oxadiazane-2,4,6-trione: short intermolecular contacts determining the crystal packing

In the title compound, C5H6N2O4, the molecules lie across a crystallographic mirror plane. The compound lacks traditional hydrogen-bond donors, and hence crystals are held together by unusual C=O...O, O...C and weak C-H...O interactions, forming layers. Adjacent layers are arranged in an antiparallel manner, yielding an ABA layer sequence. The intermolecular contacts are quite short; a topological analysis of charge density based on density-functional-theory calculations was used for consideration of these short contacts and indicated a strong attractive bonding closed-shell interaction between these atoms in the crystal structure.

Family of noble metal nitrides: First principles calculations of the elastic stability

By calculating the elastic stability using the full-potential linearized augmented plane waves (FLAPW) method, three noble metal nitrides ($\mathrm{Ir}{\mathrm{N}}_{2}$, $\mathrm{Ag}{\mathrm{N}}_{2}$, and $\mathrm{Au}{\mathrm{N}}_{2}$) were found to be stable with the fluorite structure. Together with $\mathrm{Pt}{\mathrm{N}}_{2}$, they form a new family of transition metal nitrides, where nitrogen atoms occupy all the tetrahedral interstitials of the metal sublattice, instead of larger octahedral interstitials. Using the topological analysis of charge density (atoms in molecules theory), it was shown that the stability of the new nitrides can be understood based on the simple size effect. The filling of all the small tetrahedral interstitials makes the phases difficult to compress, resulting in large bulk moduli. The frequencies of the Raman-active phonon modes were also given.

2′,4′-Dihydroxy-3-methoxy-α,β-dihydrochalcone and 2′,4-dihydroxy-α,β-dihydrochalcone: supramolecular structures formed by O—H...O, C—H...O and stacking interactions

The crystal structures of 2′,4′-di­hydroxy-3-methoxy-α,β-di­hydro­chalcone, C16H16O4, and 2′,4-di­hydroxy-α,β-di­hydro­chalcone, C15H14O3, have been determined. In both compounds, the structure consists of two nearly planar six-membered aromatic rings connected by a propanal chain, which is bent in the methoxy compound and almost straight in the other compound. In the crystal structures, the molecular units of both compounds are linked by O—H⋯O hydrogen bonds to form infinite one-dimensional chains. Hydro­gen bonds and C—H⋯O contacts in the crystal structures were studied by topological analysis of charge density based on Hartree–Fock calculations. Almost all of the investigated C—H⋯O contacts should be characterized as weak hydrogen bonds.

Topological analysis of charge density in heptasulfur imide (S 7NH) from isolated molecule to solid

Intra and intermolecular interactions of heptasulfur imide (S 7NH) are investigated in terms of topological properties analyses, such analyses are applied to both experimental (multipole model) and theoretically calculated (DFT and PDFT calculations) charge densities of the isolated molecule and of the crystal. The same analyses are also applied to a multipole model density obtained from theoretically (PDFT) derived structural amplitudes. The covalent bond character of S–N, N–H and S–S bonds are well described in terms of density, ρ b, and total energy density, H b, at the bond critical point r c, though it is clear that the S–S bonds are weaker shared interactions than those of N–H and S–N bonds. Lone pair electron regions of sulfur and nitrogen atoms are revealed as the local charge concentration site from the Laplacian of charge density. The even weaker intermolecular interactions are well characterized; these include the N–H⋯S hydrogen bonding, N⋯S binding interactions and S⋯S binding interactions. All these intermolecular binding interactions are closed-shell interactions. The Laplacian of charge density demonstrates a directional intermolecular binding interaction. The corresponding intermolecular binding energies are derived by MP2/6-311+G(d,p) calculations. Atomic graph of each atom of the molecule is described in detail by the vertices, edges and faces of the polyhedron around the nucleus to illustrate such directional interactions.

N-[2-[(3,5-di-tert-butyl-4-oxocyclohexa-2,5-dien-1-ylidene)amino]phenyl]-N-(5,7-dinitroquinolin-8-yl)-1-phenylmethanesulfonamide: the nature of intramolecular shortened contacts.

The title compound, C(36)H(35)N(5)O(7)S, is found to exist in a non-spirocyclic (ring-opened) form in the crystal, although equilibrium of ring-opened and ring-closed forms (or so-called ring-chain isomerization) is possible in solution. The 4-oxocyclohexa-2,5-diene ring has a flattened sofa conformation. The N.C intramolecular separation of the atoms which would be directly bonded in a ring-closed form is quite short [2.813 (5) A]. Topological analysis of charge density based on density-functional-theory calculations was used for consideration of shortened intramolecular contacts and indicates a strong attractive bonding interaction between these N and C atoms in the crystal structure.

Gas-phase basicities and proton affinities of alkali metal oxides and hydroxides. A theoretical study

Coupled cluster and DFT B3LYP calculations have been used to determine the structures, heats of formation, and gas-phase basicities of alkaline metal oxides M2O and hydroxides MOH, where M=Li, Na and K. Structures calculated at CCSD(T,Full)/6-31++G(2df,2pd), B3LYP/6-311+G∗∗, and B3LYP/6-311+G(3df,3pd) levels of theory were in a good agreement with each other and available experimental estimates. Atomic charges and the Bader's topological charge density analysis indicate that the bonding between M and O is ionic in all studied species. Calculated heats of formation were used to discriminate between different experimental values. Proton affinities of 1193, 1319 and 1374kJ/mol are suggested for Li2O, Na2O, and K2O, respectively.

Topological study of charge densities of impurity doped small Li clusters

A topological analysis of charge densities in ${\mathrm{Li}}_{n}\mathrm{Mg}$ and ${\mathrm{Li}}_{n}\mathrm{Be}$ clusters for $n=1\ensuremath{-}6$ is presented. ${\mathrm{Li}}_{n}\mathrm{Be}$ clusters show a stronger bonding of the Li atoms with Be, as compared to ${\mathrm{Li}}_{n}\mathrm{Mg}$ clusters. The topology of the density shows that direct bonds between Li and impurity atoms have some closed-shell nature. Li-Li bonds are observed for clusters $nl~4$ in ${\mathrm{Li}}_{n}\mathrm{Mg}$ series, while for $ng~5,$ the Li atoms form bonds only with the impurity atom. The bonds in some of the clusters seem to be strained. In contrast to Mg, the direct bonding of Be atom with the host indicates the tendency of Be to become trapped.

A topological analysis of charge density in complexes between derivatives of squaric acid and ammonium cation

A topological analysis of the electron charge density in complexes between derivatives of squaric acid and ammonium cation has been carried out. There are excellent relationships between either the charge density or its associated Laplacian at the ring critical point originated upon complexation and both geometric and energetic parameters. There is a remarkable influence of the substituents attached to the four-membered ring on the charge density at the ring critical point.

Acidity of saturated hydrocarbons

Acidities of simple saturated hydrocarbons were studied using ab initio G2 and CCSD(T)/6-311+G ∗∗, and DFT B3LYP/6-311+G ∗∗ calculations. The results suggest a 1.4 kcal/mol lower basicity for the isopropyl anion relative to the current experimental value. Charge densities of the studied neutrals, anions, and radicals were analyzed using Bader's topological charge density analysis. The acidity trends in saturated hydrocarbons were rationalized based on substituent electronegativity (field/inductive) and polarizability effects.