Electron difference densities and chemical bonding

In view of recent advances in X-ray technology it may be possible to deduce information regarding chemical bonding from experimentally determined electron densities. The construction of difference density maps represents a possible intermediate step in attaining this goal, but unresolved questions exist regarding appropriate definitions and interpretations of such maps. To shed light on these problems, theoretical difference densities are determined by ab-initio calculations for the molecules H₂, He₂, Li₂, Be₂, N₂ and F₂ at various internuclear distances. An examination of these difference density maps shows that the identification of those features of molecular electronic densities which are related to chemical bonding requires a judicious construction and a careful analysis of difference densities between molecules and their constituent atoms. Chemically relevant deformations can be small compared to density differences between different components of degenerate atomic groundstates and, consequently, chemical information can be swamped when difference densities are formed with spherically averaged atoms. To avoid such artifacts, oriented unaveraged atomic states must be subtracted for the formation of meaningful Chemical Difference Densities. The latter are explainable by means of a partitioning in terms of contributions from non-bonded inner shells, from lone pairs and from sigma and pi bonding shells. Such partitionings can be obtained through decompositions in terms of natural orbitals from correlated wavefunctions. Canonical SCF orbitals prove to be considerably less effective. Internuclear distances are found to have a great influence upon difference densities regardless of the attractive or repulsive nature of the interactions.     

Electron density calculations derived from the energy balance equation in a d.c. arc plasma burning in air

The Elenbaas-Heller equation was used to calculate the spatial distribution of electron densities ($\text{n}$_e(itR.z)) in a d.c. arc plasma burning in air at atmospheric pressure. Uranium, thorium, zirconium and a number of rare-earths were introduced as oxides into the plasma. The temperature and the electric field gradients were measured axially and radially. Electron densities were then derived from the calculated mean electrical conductivity ($\text{σ}$_(R.z)). The resulting electron density values were compared with values derived from Saha's equation for ionization processes.     

Adhesion,atomic structure,and bonding variation at TiN/VN interface by chemical segregation

Introduction of alloying elements often alters properties of materials. In the technologically significant multilayered superlattice coatings, interfaces are known to play a key role in the deformation mechanisms, especially in the phenomenon of interface‐induced superhardness at nanoscale. Here, we elucidate, by first‐principles calculations, atomic structure of TiN/VN interface and its relationship to adhesion upon introducing Cr, Mo, Ta, Y, Al, Nb, Zr, and Sc, the very commonly occurring alloying elements in the coating. We find that the elements Cr, Mo, Ta, Y weaken substantially interfacial adhesion, whereas the others modify adhesion only slightly. The bond length, charge transfer, and interactions between atoms at interface are found to be the key factors to understanding the origin of shift in properties in the coatings with the chemical alloying. Using several methods of analysis, we have clarified electronic mechanism behind the variation induced by alloying elements and determined the interfacial bonding nature to be mainly ionic with a certain degree of covalency. The theoretical calculations presented provide insight into the complex electronic properties of the TiN/VN interfaces with alloying elements. Our findings help enhance performances of the multilayered coatings for wide‐ranging applications. Copyright © 2012 John Wiley & Sons, Ltd.     

Hydrogen bonding and chemical shift assignments in carbazole functionalized isocyanides from solid-state NMR and first-principles calculations

Carbazole functionalized polyisocyanides are known to exhibit excellent electronic properties (E. Schwartz, et al., Chemistry of Materials, 2010, 22, 2597). The functionalities and properties of such materials crucially depend on the organization and stability of the polymer structure. We combine solid-state Nuclear Magnetic Resonance (NMR) experiments with first-principles calculations of isotropic chemical shifts, within the recently developed converse approach, to rationalize the origin of isotropic chemical shifts in the crystalline monomer l-isocyanoalanine 2-(9H-carbazol-9-yl) ethyl amide (monomer 1) and thereby gain insight into the structural organization of its polymer (polymer 2). The use of state-of-the-art solid-state NMR experiments combined with Density Functional Theory (DFT) based calculations allows an unambiguous assignment of all proton and carbon resonances of the monomer. We were able to identify the structure stabilising interactions in the crystal and understand the influence of the molecular packing in the crystal structure on the chemical shift data observed in the NMR spectra. Here the Nuclear Independent Chemical Shift (NICS) approach allows discriminating between 'physical' interactions amongst neighboring molecules such as ring-current effects and 'chemical' interactions such as hydrogen bonding. This analysis reveals that the isocyanide monomer is stabilized by multiple hydrogen bonds such as a bifurcated hydrogen bond involving -N-H, -C-H and O=C- moieties and Ar-H···C≡N- hydrogen bonding (Ar = aromatic group). Based on the geometrical arrangement it is postulated that the carbazole units are involved in the weak σ-π interactions giving rise to a Herringbone packing of the molecules. The chemical shift analysis of the polymer spectra readily establishes the existence of N-H···O=C hydrogen bonds despite the limited resolution exhibited by the polymer spectra. It is also elucidated that the relative arrangement of the carbazole units in the polymer differs significantly from that of the monomer.     

Electron pairing and chemical bonds. Molecular structure from the analysis of pair densities and related quantities

The Fermi holes are presented as a new means of analysis and visualisation of molecular structure. Based on these quantities it is possible to get clear and highly visual insight into the structure of molecular fragments (functional groups) even in molecules with complex bonding patterns like multicenter bonding, hypervalence, etc. In addition to allowing the detection and localization of multicenter bonding, the new approach also brings some new interesting possibilities for the quantitative evaluation of molecular similarity. This revised version was published online in July 2006 with corrections to the Cover Date.     

Partial LCAO densities of states for ScN,TiN, ZrN and ScP

Densities of states (DOS) and partial densities of states were calculated from self-consistent APW band structure calculations for four transition metal compounds (ScN, TiN, ZrN and ScP) using a recently published improved LCAO interpolation scheme. The total DOS and the LCAO non local partial metal s, p and d and non-metal s and p DOS of these compounds are presented and compared with non local LCAO partial DOS from earlier calculations as well as with local partial DOS obtained directly from the APW or LAPW wave functions. A LCAO charge analysis for all valence states and for the individual valence bands is also given.     

Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations

Polyglutamine (polyQ) diseases, including Huntington’s disease (HD), are caused by expansion of polyQ-encoding repeats within otherwise unrelated gene products. The aggregation mechanism of polyQ diseases, the inhibition mechanism of Congo red, and the alleviation mechanism of trehalose were proposed here based on quantum chemical calculations and molecular dynamics simulations. The calculations and simulations revealed the following. The effective molecular bonding is between glutamine (Gln) and Gln (Gln + Gln), between Gln and Congo red (Gln + Congo red), and between Gln and trehalose (Gln + trehalose). The bonding strength is −13.1 kcal/mol for Gln + Gln, −24.4 kcal/mol for Gln + Congo red, and −12.0 kcal/mol for Gln + trehalose. In the polyQ region, both the number of intermolecular Gln + Gln formations and the total calories generated by the Gln + Gln formation are proportional to the number of repetitions of Gln. We propose an aggregation mechanism whose heat generated by the intermolecular Gln + Gln formation causes the pathogeny of polyQ disease. In our aggregation mechanism, this generated heat collapses the host protein and promotes fibrillogenesis. Without contradiction, our mechanism can explain all the experimental results reported to date. Our mechanism can also explain the inhibition mechanism by Congo red as an inhibitor of polyglutamine-induced protein aggregation and the alleviation mechanism by trehalose as an alleviator of that aggregation. The inhibition mechanism by Congo red is explained by the strong interaction with Gln and by the characteristic structure of Congo red.     

Nitrogen-doped TiO2 from TiN and its visible light photoelectrochemical properties

Homogeneous titanium nitride (TiN) thin film was produced by simple electrophoreic deposition process on Ti substrate in an aqueous suspension of nanosized TiN powder. Nitrogen-doped titanium dioxide (TiO_2−xN_x) was synthesized by oxidative annealing the resulted TiN thin film in air. Photoelectrochemical measurements demonstrated visible light photoresponse for the electrode of annealed electrophoreic deposited TiN samples. It is found that the synthesized TiO_2−xN_x electrode showed higher photo potential under white and visible light illumination than the pure TiO₂ electrode. The photocurrent under visible light illumination was also observed, which increased with the increase of deposition time of TiN thin films.     

XeCu covalent bonding in XeCuF and XeCuCl, characterized by fourier transform microwave spectroscopy supported by quantum chemical calculations

XeCu covalent bonding has been found in the complexes XeCuF and XeCuCl. The molecules were characterized by Fourier transform microwave spectroscopy, supported by MP2 ab initio calculations. The complexes were prepared by laser ablation of Cu in the presence of Xe and SF(6) or Cl(2) and stabilized in supersonic jets of Ar. The rotational constants and centrifugal distortion constants show the XeCu bonds to be short and rigid. The (131)Xe, Cu, and Cl nuclear quadrupole coupling constants indicate major redistributions of the electron densities of Xe and CuF or CuCl on complex formation which cannot be accounted for by simple electrostatic effects. The MP2 calculations corroborate the XeCu bond lengths and predict XeCu dissociation energies approximately 50-60 kJ mol(-)(1). The latter cannot be accounted for in terms of induction energies. The MP2 calculations also predict valence molecular orbitals with significant shared electron density between Xe and Cu and negative local energy densities at the XeCu bond critical points. All evidence is consistent with XeCu covalent bonding.     

Electron deformation density in titanium diboride chemical bonding in TiB2

Titanium diboride, TiB₂, crystallizes in the AlB₂-type structure, hexagonal P6/mmm. The conventional, free atom crystal structure refinement led to R=2.23%, and including extinction corrections to R=1.58%. Multipole refinements with multipoles up to order four (hexadecapole) reduced the R value to 1.21%. Difference density maps revealed charge deficiencies on the boron sites and broadbands of charge accumulations between the boron atoms indicating a graphitic B-delocalization of the boron sp² hybrid orbitals.     

Interatomic interactions in momentum space. Momentum density and kinetic energy in chemical bonding

On the basis of the virial theorem for a uniform scaling process of a polyatomic system, the total energy and its gradient are quantitatively related with the behavior of the electron density in momentum space through the kinetic energy of the system. For attractive and repulsive interactions, the behavior of the momentum density distribution and its effect on the stabilization energy and the interatomic force are examined. Some guiding principles are deduced for their interrelation. The results are used to clarify the role of kinetic energy in chemical bonding. Possible energy partitioning in this approach is also mentioned.     

Synthesis and photonic band calculations of NCP face-centered cubic photonic crystals of TiO2 hollow spheres

With the help of self-assembly, thermal sintering, selective etching techniques and sol-gel process, the non-close packed (ncp) face-centered cubic (fcc) photonic crystals of titanium dioxide (TiO2) hollow spheres connected by TiO2 cylindrical tubes have been fabricated using silica template. The photonic bandgap calculations indicate that the ncp structure of TiO2 hollow spheres was easier to open the pseudogaps than close packed system at the lowest energy.     

Interfacial bonding,energy dissipation,and adhesion

Thin sheets of several elastomers have been adhered together by C? C or S? S interfacial bonds and peeled apart at various rates and temperatures. For C? C bonding, values of the work G required per unit area to separate the sheets could be superposed to form a master curve versus peel rate using Williams-Landel-Ferry (WLF) temperature shift factors. Threshold values G_o at low rates and high temperatures ranged from virtually zero for nonbonded sheets up to the tear strength of the sheet itself, 50-80 J/m², for fully interlinked sheets, in proportion to the density of interfacial bonds. The strength thus appears to be the sum of two terms: G_o and a viscoelastic loss function which itself is approximately proportional to G_o. By comparing the dependence of G upon rate of peel with the dependence of dynamic shear modulus μ′ upon oscillation frequency, an effective length of the fracture zone was deduced. It was extremely small in all cases, only about 1 Å. With sulfur interlinks, values of G were larger at all peel rates and varied more with temperature than predicted by the WLF relation. This is attributed to a concomitant decrease in S? S bond strength with temperature, and an increase in energy dissipation as the weaker sulfur bonds fail. © 1994 John Wiley & Sons, Inc.     

Additivity model calculations of UHF spin densities and charge densities in methyl-substituted radical cations

By use of a heteroatom model for the methyl group and an additivity model for spin densities, the unrestricted Hartree-Fock after annihilation (UHFAA) results for the radical cations of naphthalene, 1-methylnaphthalene and 2-methylnaphthalene are used to predict the spin densities in the -electron approximation in the corresponding cations of di-, tri- and tetramethylnaphthalenes. The additivity model approach is shown to be equally successful for charge densities.     

Structure and morphology of nylon 46 lamellar crystals: Electron microscopy and energy calculations

A detailed electron microscopy study of the structure and morphology of lamellar crystals of nylon 46 obtained by crystallization from solution has been carried out. Electron diffraction of crystals supported by X‐ray diffraction of their sediments revealed that they consist of a twinned crystal lattice made of hydrogen‐bonded sheets separated 0.376 nm and shifted along the a‐axis (H‐bond direction) with a shearing angle of 65°. The interchain distance within the sheets is 0.482 nm. These parameters are similar to those previously described for nylon 46 lamellar crystals grown at lower temperatures. A combined energy calculation and modeling simulation analysis of all possible arrangements for the crystal‐packing of nylon 46 chains, in fully extended conformation, was performed. Molecular mechanics calculations showed very small energy differences between α (alternating intersheet shearing) and β (progressive intersheet shearing) structures with energy minima for successive sheets sheared at approximately 1/6 c and 1/3 c. A mixed lattice composed of a statistical array of α and β structures with such sheet displacements was found to be fully compatible with experimental data and most appropriate to describe nylon 46 lamellar crystals. Annealing of the crystals at temperatures closely below the Brill transition induced enrichment in β structure and increased chain‐folding order. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 41–52, 2000     

Electron distribution and chemical bonding in M3(XO4)2 molecules (M = Mg, Cu; X = P, V) as determined by Ab initio calculations

Ab initio quantum-chemical calculations of cage molecules M₃(XO₄)₂ (M = Mg, Cu; X = P, V) have been carried out. Interatomic interactions in them are quantitatively characterized based on analysis of the electronic properties at the critical points in electron density. The Mg-O interaction is close to pure closed-shell interactions, whereas the other interactions can be treated as intermediate with different degrees of covalence. The specific features of the electronic structure of the molecules are revealed with the use of the electron pair localization function. The arrangement of electron pairs in the outer shells of the cores of the transition metals Cu and V corresponds to the Gillespie model of the regions of local concentration of electrons located opposite the ligands, which illustrates the mechanism of bonding of atoms of the third and subsequent periods of the periodic table.