Orbital overlap and chemical bonding

The chemical bonds in the diatomic molecules Li(2)-F(2) and Na(2)-Cl(2) at different bond lengths have been analyzed by the energy decomposition analysis (EDA) method using DFT calculations at the BP86/TZ2P level. The interatomic interactions are discussed in terms of quasiclassical electrostatic interactions DeltaE(elstat), Pauli repulsion DeltaE(Pauli) and attractive orbital interactions DeltaE(orb). The energy terms are compared with the orbital overlaps at different interatomic distances. The quasiclassical electrostatic interactions between two electrons occupying 1s, 2s, 2p(sigma), and 2p(pi) orbitals have been calculated and the results are analyzed and discussed. It is shown that the equilibrium distances of the covalent bonds are not determined by the maximum overlap of the sigma valence orbitals, which nearly always has its largest value at clearly shorter distances than the equilibrium bond length. The crucial interaction that prevents shorter bonds is not the loss of attractive interactions, but a sharp increase in the Pauli repulsion between electrons in valence orbitals. The attractive interactions of DeltaE(orb) and the repulsive interactions of DeltaE(Pauli) are both determined by the orbital overlap. The net effect of the two terms depends on the occupation of the valence orbitals, but the onset of attractive orbital interactions occurs at longer distances than Pauli repulsion, because overlap of occupied orbitals with vacant orbitals starts earlier than overlap between occupied orbitals. The contribution of DeltaE(elstat) in most nonpolar covalent bonds is strongly attractive. This comes from the deviation of quasiclassical electron-electron repulsion and nuclear-electron attraction from Coulomb's law for point charges. The actual strength of DeltaE(elstat) depends on the size and shape of the occupied valence orbitals. The attractive electrostatic contributions in the diatomic molecules Li(2)-F(2) come from the s and p(sigma) electrons, while the p(pi) electrons do not compensate for nuclear-nuclear repulsion. It is the interplay of the three terms DeltaE(orb), DeltaE(Pauli), and DeltaE(elstat) that determines the bond energies and equilibrium distances of covalently bonded molecules. Molecules like N(2) and O(2), which are usually considered as covalently bonded, would not be bonded without the quasiclassical attraction DeltaE(elstat).     

Synthesis, structure and reactivity of organogold compounds of relevance to homogeneous gold catalysis

Organogold(I) phosphane complexes were prepared, their structure was investigated and their reactivity in reactions with Michael acceptors, sources of electrophilic halogens and protons were investigated.     

Simulating periodic trends in the structure and catalytic activity of coinage metal nanoribbons

We present a systematic density functional theory (DFT) study of the structure and catalytic activity of group 10 (Ni, Pd, Pt) and group 11 (Cu, Ag, Au) coinage metal nanoribbons. These infinite, periodic, quasi‐one‐dimensional structures are conceptually important as intermediates between small metal clusters and close‐packed metal surfaces, and have been shown experimentally to be practical catalysts. We find that nanoribbons have significantly higher predicted H₂ dissociation activity than close‐packed metal surfaces consistent with their lower coordination numbers. Computed periodic trends are reasonable, with late transition states and low barriers for H₂ dissociation over late group 10 nanoribbons, suggesting their promise as practical catalysts. These trends are consistent with the isolated nanoribbons' computed molecular electrostatic potentials. Calculations also predict nearly linear Brønsted–Evans–Polanyi relationships between the nanoribbons' H₂ dissociation energies and dissociation barriers. We also test new meta‐generalized gradient approximation (GGA) and hybrid DFT approximations for H₂ dissociation over these nanoribbons. These new functionals increase the (generally underestimated) dissociation barriers predicted by standard GGAs, motivating their continued application in surface chemistry. © 2015 Wiley Periodicals, Inc.     

Titanium hydrazido and imido complexes: synthesis, structure, reactivity, and relevance to alkyne hydroamination

Treatment of Ti(NMe(2))(2)(dpma) (1) with aniline results in the protonation of the dimethylamido ligands, which are retained as dimethylamines, and generation of a titanium imido complex Ti(NPh)(NHMe(2))(2)(dpma) (2) in 94% yield. The monomeric imido 2 is converted to the reactive dimeric micro-imido [Ti(NPh)(dpma)](2) (3) on removal of the labile dimethylamine donors. The dimer 3 is converted to monomeric terminal imido complexes in the presence of added donors, e.g., 4,4'-di-tert-butyl-2,2'-bipyridine (Bu(t)-bpy) and DME. Compounds 1-3 exhibit the same rate constant for 1-phenylpropyne hydroamination by aniline and are all kinetically competent to be involved in the catalytic cycle. Attempts to use 1 as a catalyst for hydroaminations involving 1,1-dimethylhydrazine resulted in only a few turnovers under the best conditions. Consequently, the chemistry of 1 with hydrazines to generate hydrazido complexes was scrutinized for comparison with the imido species. Through these studies, titanium hydrazido complexes including Ti(eta(2)-NHNC(5)H(10))(2)(dpma) (5), Ti(eta(2)-NHNMe(2))(2)(dpma) (6), and [Ti(micro:eta(1),eta(2)-NNMe(2))(dpma)](2) (7) were characterized. In addition, a terminal hydrazido(2-) complex was available by addition of Bu(t)-bpy to 1 prior to 1,1-dimethylhydrazine addition, which provided Ti(eta(1)-NNMe(2))(Bu(t)-bpy)(dpma) (8). Compound 8 was structurally characterized and compared to Ti(NPh)(Bu(t)-bpy)(dpma) (4b), an imido derivative with the same ancillary ligand set. Compound 8 has a nucleophilic beta-nitrogen consistent with a hydrazido(2-) formulation, as determined by reaction with MeI to form the ammonium imido complex [Ti(NNMe(3))(Bu(t)-bpy)(dpma)]I (9). Analogous pyridinium imido complexes [Ti(N-1-pyridinium)(Bu(t)-bpy)(dpma)](+) (10) are available by addition of 1-aminopyridinium iodide to 1. From the investigations, some conclusions regarding the activity of titanium pyrrolyl complexes in hydroamination were drawn. The lack of conversion of the bis[micro-hydrazido(2-)] 7 to monomeric species in the presence of donor ligands is put forth as one explanation for the poor hydrazine hydroamination activity of 1. This problem was combated in the synthesis of Ti(NMe(2))(2)(dap)(2), which is an active catalyst for hydrazine hydroamination of alkynes.     

How to use the vibrational data for a better understanding of bonding structure and reactivity of organometallic complexes

The infrared frequency and intensity values of the main vibrational modes of selected examples of hydrocarbon ligands bonded to metals are reported. Despite the approximations on the vibrational analysis, the data offer fundamental information on structure, bonding, and reactivity of the metal-ligand unit, successfully comparable with those obtained by other sources (structural analysis, nmr spectroscopy, MO calculation). A future extension of this topic to the study of the adsorbate surface interaction is proposed, in light of the well-known cluster-surface analogy.     

Synthesis,crystal structure,and reactivity of alkali and silver salts of sulfonated imidazoles

Both 2-methylimidazole and 2-ethyl-4-methylimidazole were monosulfonated with oleum in the five position. In crystals of the monohydrate of 2-methylimidazole-5-sulfonic acid, hydrogen bonds link the molecules into a 3-dimensional network, while in crystals of 2-ethyl-4-methylimidazole-5-sulfonic acid, corrugated 2-dimensional layers are present. The Li and Ag salts and the bis(trimethylsilyl) derivatives of 2-ethyl-4-methylimidazole-5-sulfonic acid were prepared, and there is evidence for doubly deprotonated imidazolesulfonate in aqueous solution. The monohydrate of the Li salt and the Ag salt also form a 3-dimensional, H-bonded network. Only in the Ag salt does the asymmetric unit consist of more than one basic formula unit. One Ag atom is 2-coordinate and links two nitrogen atoms, while the other Ag atom has distorted tetrahedral coordination and links the sulfonate groups into an infinite chain. Reactions of the silver salt with 1,4-dibromobutane in non-protic solvents such as 1-methyl-2-pyrrolidone were used to link two of the imidazolesulfonic acid units with a 4-carbon chain at the nitrogens.     

Synthesis and novel reactivity of halomethyldimethylsulfonium salts

Iodomethyl-, chloromethyl-, and fluoromethyldimethylsulfonium salts, 4b-d, have been synthesized and are observed to be highly reactive molecules that exhibit extraordinary diversity with respect to the nature of their reactivity, undergoing facile direct substitution (S(N)2) reactions, but also being highly susceptible to electron-transfer reactions. Cyclic voltametry experiments indicated that the iodomethyldimethylsulfonium compound, 4b, is a potent electron acceptor, even surpassing the reactivity of perfluoro-n-alkyl iodides in that capacity. The iodo- and chloromethyldimethylsulfonium salts, 4b,c, as well as the analogous iodomethyltrimethylammonium salt, 3a, are shown to be reactive SET acceptors.     

Synthesis and reactivity of furazanyl- and furoxanyldiazonium salts

Diazotization of aminofurazans (1) and 4-aminofuroxans (2) with nitrosylsulfuric acid in a mixture of conc. H₂SO₄ and H₃PO₄ has been studied and offered as a general method for preparing furazanyl- (3) and furoxanyldiazonium (4) salts. It has been shown that reactions with the retention of the N-N-group (azo coupling, formation of triazenes and azides) are typical of salts3 and4, while elimination of the N₂ molecule (Sandmeyer reaction, hydrolysis, reduction) is not typical.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1949–1953, November, 1993.     

Synthesis, structure, and reactivity of a dinuclear metal complex with linear M-H-M bonding

Reaction of two equiv of 1-adamantylzinc bromide with (dippm)NiBr2 (dippm = bis(di-isopropylphosphino)methane) led to a dinuclear metal complex containing a unique linear bridging hydride ligand. The hydride was characterized by neutron diffraction methods, which confirmed a linear bonding mode. Preliminary reactivity studies of this unusual dimer are reported.     

Isomerization and oxygen atom transfer reactivity in oxo-Mo complexes of relevance to molybdoenzymes

Both dioxo Mo(VI) and mono-oxo Mo(V) complexes of a sterically restrictive N2O heteroscorpionate ligand are found to exist as cis and trans isomers. The thermodynamically stable isomer differs for the two oxidation states, but in each case, we have isolated the kinetically labile isomer and followed its isomerization to the thermodynamically stable form. The Mo(VI) complex is more stable in the cis geometry and isomerizes more than 6 times faster than the Mo(V) complex, which prefers the trans geometry. In OAT reactions with PPh3, the trans isomer of the dioxo-Mo(VI) reacts approximately 20 times faster than the cis isomer. Thus, there are both oxidation state and donor atom dependent differences in isomeric stability and reactivity that could have significant functional implications for molybdoenzymes such as DMSO reductase.     

Benzotriazol-1-ylmethylammonium salts synthesis and reactivity

Benzotriazol-1-ylmethylamines on treatment with alkylating agents afford benzotriazol-1-ylmethylammoni-um salts, also available from reactions of chloromethylbenzotriazole with tertiary amines. In deuterated solvents under basic conditions the methylene protons of these salts exchange with deuterium. At elevated temperatures, an alkyl group substituent migrated from the ammonium center to the benzotriazolyl N-3. Reactions of the salts with Grignard reagents afforded various products arising from substitution of the ammonium moiety and/or from attack on the benzotriazolyl N-3 or on the benzenoid ring.     

Understanding the electronic structure, reactivity, and hydrogen bonding for a 1,2-diphosphonium dication

The experimental charge density for hexamethyldiphosphonium ditriflate has been determined from low-temperature high-resolution X-ray diffraction data. These results have been compared with theoretically calculated values for the isolated gas-phase compound. Analysis of the topological and atomic basin properties has provided insight into the exact nature of the P-P bond in both the crystalline and the gas-phase structures. The rho(b)(r) and nabla2rho(b)(r) values highlight the covalent nature of the P-P bond, while the atomic charges indicate a localization of the positive charges on the two phosphorus atoms. This seems to indicate that a covalent bond is formed despite a strong electrostatic repulsion between these two heteroatoms. The topological properties and electrostatic potentials have also been shown to provide significant insight into the chemical reactivity of the title compound. A topological analysis of P2Me4, P2Me5(+), and P2Me6(+2) species has provided information about the progression of the P-P bond in the synthesis of the title compound. An investigation of the different hydrogen-bonding networks present in the crystalline and gas-phase structures, along with their affect on the electronic structure of the title compound has also been investigated. This has all led to significant new insight into the electronic structure, reactivity, and weak hydrogen bonding in prototypical 1,2-diphosphonium dications.     

Effect of dielectric properties and structure of aqueous solutions of diallylammonium salts on their reactivity in radical polymerization

The complex dielectric permittivity in the frequency range 7.5–25.0 GHz and the low-frequency specific conductivity of aqueous solutions of diallylammonium salts (diallylammonium and diallylmethylammonium trifluoroacetates and diallyldimethylammonium chloride) were measured at 293–308 K over a wide concentration range. On the basis of the results, the parameters of dielectric relaxation were calculated. The number of water molecules in the solvation shell of the salts was estimated. The concentration behavior of the initial rate of radical polymerization of diallylammonium salts and the rate constant of bimolecular chain termination was correlated with the specific features of the structure of aqueous monomer solutions. The role of “free” water in the initial salt solutions was revealed, a species whose presence in the system determines the character of concentration behavior of the rate constants for the elementary steps of polymerization, such as propagation, chain transfer to the monomer, and bimolecular chain termination.     

Some periodic trends,molecular structure,normal coordinate analysis of 1,3,5-trioxane, -trithiane and -triselenane: computational and vibrational studies

The Raman (3200–100 cm⁻¹) and infrared spectra (3200–200 cm⁻¹) of solid C₃H₆O₃ (TO) and C₃H₆S₃ (TS) have been recorded and only the chair conformation is present. Furthermore, utilizing the CH stretching bands at the infrared spectrum of the gaseous phase, the CH_ax and CH_eq distances are found to be 1.088 and 1.107 Å, respectively. The structural parameters and conformational stabilities for 1,3,5-C₃H₆X₃ series (where X=O, S and Se atoms) have been obtained from density functional theory at the Becke3-LYP gradient-corrected functional (DFT-B3LYP) and from MP2 level with full electron correlation. These calculations have been extended up to 6-311++G(d,p) basis set to include polarization and diffusion functions. All computational results and vibrational analysis are in favor of the chair conformation (C_3v), whereas the boat (C₁) and Planar (D_3h) forms have been excluded owing to the predicted imaginary wavenumber(s). According to 6-311++G(d,p) basis set, the ring size and the tendency of the ring to undergo flattening is found to be directly proportional to the atomic size of the substituted hetero atoms (X) of the chair. The calculated DFT-B3LYP scaled quantum chemistry (QC) force fields at 6-31G(d) basis set lead to a number of revised assignments for certain vibrational modes and it appears to give quite accurate Raman spectra for the investigated chalcogenanes. The estimated bond lengths, bond angles, rotational constants, Raman activities dipole moment and unscaled force constants are compared with either theoretical and/or experimental results whenever possible.     

Secondary structure analysis of peptides with relevance to iron–sulfur cluster nesting

Peptides coordinated to iron–sulfur clusters, referred to as maquettes, represent a synthetic strategy for constructing biomimetic models of iron–sulfur metalloproteins. These maquettes have been successfully employed as building blocks of engineered heme-containing proteins with electron-transfer functionality; however, they have yet to be explored in reactivity studies. The concept of iron–sulfur nesting in peptides is a leading hypothesis in Origins-of-Life research as a plausible path to bridge the discontinuity between prebiotic chemical transformations and extant enzyme catalysis. Based on past biomimetic and biochemical research, we put forward a mechanism of maquette reconstitution that guides our development of computational tools and methodologies. In this study, we examined a key feature of the first stage of maquette formation, which is the secondary structure of aqueous peptide models using molecular dynamics simulations based on the AMBER99SB empirical force field. We compared and contrasted S…S distances, [2Fe-2S] and [4Fe-4S] nests, and peptide conformations via Ramachandran plots for dissolved Cys and Gly amino acids, the CGGCGGC 7-mer, and the GGCGGGCGGCGGW 16-mer peptide. Analytical tools were developed for following the evolution of secondary structural features related to [Fe-S] cluster nesting along 100 ns trajectories. Simulations demonstrated the omnipresence of peptide nests for preformed [2Fe-2S] clusters; however, [4Fe-4S] cluster nests were observed only for the 16-mer peptide with lifetimes of a few nanoseconds. The origin of the [4Fe-4S] nest and its stability was linked to a “kinked-ribbon” peptide conformation. Our computational approach lays the foundation for transitioning into subsequent stages of maquette reconstitution, those being the formation of iron ion/iron–sulfur coordinated peptides. © 2018 Wiley Periodicals, Inc.     

Structural trends and chemical bonding in Te-doped silicon clathrates

The recently discovered tellurium-doped silicon clathrates, Te7+xSi20-x and Te16Si38, both low- and high-temperature forms (cubic and rhombohedral, respectively), exhibit original structures that are all derived from the parent type I clathrate G8Si46 (G = guest atom). The similarities and differences between the structures of these compounds and that of the parent one are analyzed and discussed on the basis of charge distribution and chemical bonding considerations. Because of the particular character of the Te atom, these compounds appear to be at the border between the clathrate and polytelluride families.     

Synthesis and reactivity of the Tl1 salts of

Synthons Tl1[TCNE]*- (1) and Tl12[TCNE]2- (2), for [TCNE]*- and [TCNE]2-, respectively, in metathesis reactions have been quantitatively prepared and characterized. The structure of 1 was solved and refined in a monoclinic unit cell at 27 degrees C [C2/c, a = 12.6966 (12) angstroms, b=7.7599 (7) angstroms, c=15.5041 (15) angstroms, beta = 96.610 (5) degrees , V= 1517.4 (2) angstroms3, Dcalcd = 2.911 gcm-3, Z=8, R1 = 0.0575, omegaR2=0.0701] and exhibits nuCN absorptions at 2,191 (s) and 2,162 (s) cm-1 consistent with metal-bound [TCNE]*-. The structure of 1 consists of a distorted square antiprismatic octacoordinate Tl1 bound to six monodentate [TCNE]*-s with TlN separations ranging from 2.901 to 3.171 angstroms averaging 3.020 angstroms, and one bidentate [TCNE]*- with TlN separations averaging 3.279 angstroms. The TlN bonding is attributed to electrostatic bonding. The [TCNE]*-s form dimerized zigzag chains with intra- and interdimer separations of 2.87 and 3.29 angstroms, respectively. The tight pi-[TCNE](2)2- dimer is diamagnetic and has the shortest intradimer [TCNE]*- distance reported. These synthons for [TCNE]*- and [TCNE]2- in metathesis reactions lead to the precipitation of, for example, TlIX (X = Cl, Br, OAc). Reaction of 1 with MnIII(porphyrin)X (X = Cl, OAc) forms the molecule-based magnets of [MnIII(porphyrin)][TCNE] composition, while the reaction of [CrI(C6H6)2]Br and (Me2N)2CC(NMe2)2Cl2, [TDAE]Cl2, with 1 forms [CrI(C6H6)2] [TCNE] and [TDAE][TCNE]2, respectively. The structure of [TDAE][TCNE]2.MeCN was solved and refined in an orthorhombic unit cell at 21 degrees C [I222, a = 10.2332(15), b = 13.341(6), c = 19.907(8) angstroms, V= 2717.7 angstroms3, Z = 4; Dcalcd = 1.216 gcm-3, R=0.083, Romega = 0.104] and exhibits upsilonCN absorptions at 2,193 (m), 2,174 (s), and 2,163 (s) cm-1 consistent with isolated [TCNE](2)2- , in contrast to the aforementioned TlI bound [TCNE](2)2-. The reaction of 2 with [TDAE]Cl2 forms [TDAE]2+[TCNE]2-.