A look at bonds and bonding

Structural Chemistry - Even after roughly a century of quantum theory, there is still debate, sometimes rather contentious, as to the nature of the chemical bond—or is it bonds, or is it...     

Another look at the degree‐Kirchhoff index

Let G be an arbitrary graph with vertex set {1,2, …,N} and degrees d_i ≤ D, for fixed D and all i, then for the index R′(G) = ∑_{i < j}d_id_jR_ij we show that We also show that the minimum of R′(G) over all N‐vertex graphs is attained for the star graph and its value is 2N² ? 5N + 3. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Another look at magic-angle-detected fluorescence and emission anisotropy decays in fluorescence microscopy

It is shown that in contrast to a traditional fluorescence spectroscopy with the parallel beams of light, in which the kinetic fluorescence decays are collected at the so-called magic-angle of thetamag=54.7 degrees, in the fluorescence microscopy, the value of the magic-angle depends on the numerical aperture (NA) of a microscope objective and on the refractive index (n) of an immersion liquid used. Two methods enabling the determination of the magic-angle values corresponding to different values of NA/n, are discussed. It is shown that thetamag changes from a value of 54.7 degrees at the NA/n-->0, to a value of 45 degrees with NA/n-->1. Also in contrast to a traditional fluorescence spectroscopy, in the fluorescence microscopy the term I parallel(t)+2I perpendicular (t) does not represent the total fluorescence intensity Itot(t), because the resulting fluorescence decay I parallel(t)+2I perpendicular (t) is contributed by the dynamic evolution of excited fluorophores. A correctly defined total fluorescence intensity solely represents the kinetic evolution of excited fluorophores, and in the fluorescence microscopy it equals Itot(t)=3Imag(t), where Imag(t) represents the fluorescence intensity detected at thetamag corresponding to a particular NA/n value. If the correct (true) decay of Itot(t) is substituted into the denominator in the expression for the emission anisotropy r(t), r(t) is a (multi)exponential function of time and it accounts for the high-aperture excitation-detection conditions.     

A new look at bonding in trialuminides: reinvestigation of TaAl3

Single crystals of TaAl3 were grown at high temperatures from an Al-rich, binary solution. TaAl3 adopts the D0(22) structure type, space group I4/mmm with a=3.8412(5) A, c=8.5402(17) A, and Z=2. The structure type, which is the preferred structure for all group 5 trialuminides and TiAl3 as well as the high-temperature form of HfAl3, is a binary coloring of the face-centered-cubic (fcc) arrangement. The distribution of Ta atoms creates a three-dimensional network of vertex and edge-sharing square pyramids of Al atoms. Temperature-dependent electrical resistivity and magnetic susceptibility measurements are consistent with TaAl3 being a metallic compound with a relatively low density of states at the Fermi surface. Furthermore, tight-binding electronic structure calculations are utilized to describe the bonding in these compounds and to compare their stability with respect to the alternative fcc-related, e.g., the D0(23) (ZrAl3-type) and the L1(2) (AuCu3-type), structures. A modified Wade's rule argument provides insights into the structural preferences.     

Another look at the melting temperature of colloidal crystals in the completely deionized suspension

Melting temperature (T _m) of colloidal crystals of monodispersed polystyrene and silica spheres has been measured for thecompletely deionized suspensions as a function of sphere concentration. More than 3 weeks are needed before achievement of the completely deionized state.T _mincreases substantially as the deionization process of the suspension proceeds. The most reliable values ofT _mobserved for the completely deionized suspensions are successfully analyzed again with the theory of Williams et al. The newT _mvalues are compared also with the theory of Robbins et al., which treats the repulsive Yukawa potential between colloidal spheres.     

Another Look at Long-Chain Branching

Long-chain branching can occur during radical polymerization and is especially important for polyethylene. An improved method of calculating the effect of long-chain branching on molecular weight distribution is presented. This method uses a probability treatment. The results are more consistent with both kinetic theory and experimental data than the results of previous long-chain branching calculations. In contrast to previous calculations, the present work shows that generation cannot occur from long-chain branching alone.     

A discrete look at localization

This article introduces a set of localized orthonormal functions to serve as basis functions for quantum calculations. They are defined to be eigenfunctions of the position operator in a function space. Their properties, including their variances, for a one-dimensional system are developed. The application to simple harmonic motion is considered as an example and, in particular, the time evolution of an initially localized function is calculated and shown to be periodic. The theory can be interpreted as producing a discrete quantization of space with Hamiltonian interactions that are predominantly between nearest neighbors. These functions can also be used in approximate calculations. To illustrate their accuracy, the example of a Morse oscillator treated as a perturbation of a harmonic oscillator is reconsidered. It is shown that the localized functions in a variational calculation lead to a result that is a good approximation for the lowest states. Furthermore, the use of a wave function that is defined only at discrete points can be justified as the first approximation to this, so that its accuracy can also be discussed. © 1995 John Wiley & Sons, Inc.     

Hydrogen bonding in phenols—VIII: Intermolecular hydrogen bonds of phenol and alkylisothiocyanates

The H-bonding between the phenol and a series of alkylisothiocyanates has been studied over a range of temperatures. Association constants for the systems phenol-isothiocyanates were determined from IR spectre. Enthalpies and entropies of association were estimated from the tempperature-dependencies of the association constants. The -ΔH values of the systems studied in the range of 1·7–2·8 Kcal/mole indicate weaker H-bonding than those reported for the systems phenolalkylthiocyanates.     

Electrophilic addition reactions at multiple bonds

Conclusions A new reaction was discovered when alkoxyalkyl and acyl cations are reacted with alkynes in a nitroalkane medium, which proceeds on the type of a conjugated addition involving the nitroalkane, and leads to the formation of polyfunctional derivatives.See [1] for Communication 6.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 10, pp. 2232–2235, October, 1972.     

A fresh look at aromatic dianions

Isolated dianions of cyclooctatetraene and cyclobutadiene are, despite their aromatic character, unstable with respect to electron loss. Here we present the first ab initio study of the autodetachment lifetimes of several "aromatic" dianions. In particular, we investigate whether aromatic pi systems are associated with an enhanced stability with respect to electron loss and whether cross-conjugated (Y-aromatic) hydrocarbon dianions possess longer lifetimes than their linear-conjugated isomers. Moreover, our results are compared with bound state calculations for these metastable dianions, allowing us to analyze the validity of the latter approach. All considered, hydrocarbon dianions are found to possess surprisingly short autodetachment lifetimes on the order of a few femtoseconds, and therefore only electron scattering techniques seem to be capable of observing these species in the gas phase. The trends of the computed energies and lifetimes are best understood in terms of the mutual Coulomb repulsion of the extra charges. Small gas phase dianions can only be stable if the excess electrons can localize at least at two subgroups of high local electron affinity. Adding both extra electrons into one delocalized pi system leads to a very unstable species, and thus especially those structures associated with pronounced aromaticity are found to show high energies and short lifetimes.     

A fresh look at natural tropolonoids

Tropones and tropolones have been of increasing interest in the past few years; approximately 200 such materials occur in nature. This article reviews the distribution of these materials, the biosynthetic pathways for their production and their biological activities. There are 154 references.     

A closer look at analytical signals

Analytical chemistry will be considered here as the measurement science of chemistry that generates, treats, and evaluates signals which contain information about the composition and structure of samples. Analytical information is always obtained from signals. Characteristics and peculiarities of analytical signals will be considered from a very general point of view. A mathematical model of the influencing of signals will be given from which essential performance characteristics of analytical methods can be derived, e.g. sensitivity, cross-sensitivity, specificity, selectivity, and ruggedness (robustness).     

A detailed look at vesicle fusion

Many different hypotheses on the molecular mechanisms of vesicle fusion exist. Because these mechanisms cannot be readily asserted experimentally, we address the problem by a coarse-grained molecular dynamics simulations study and compare the results with the results of other techniques. The simulations performed include the fusion of small and large vesicles and exocytosis, i.e., the fusion of small vesicles with flat bilayers. We demonstrate that the stalk, the initial contact between two fusing vesicles, is initiated by lipid tails that extend spontaneously. The stalk is revealed to be composed of the contacting monolayers only, yet without hydrophobic voids. Anisotropic and radial expansion of the stalk have been theorized; we show that stalk evolution can proceed via both pathways starting from similar setups and that water triggers the transition from elongated stalk to hemifusion diaphragm.     

A new three-center model for diatomic bonds based on the spherical Gaussian bonding function

A new three-center model for diatomic bonds is proposed based on the spherical Gaussian bonding function. The characteristics of the model are that the magnitude of effective bond-charge described by the function is different for different observation points, and that the position of the bond-charge on the bond axis satisfies the energy variation principle.

According to the model and two additional assumptions, some theoretical formulas for bond properties, such as the total energy of system, dissociation energy, dipole moment, force constant and field gradients at nuclei, are derived. The calculated results are basically in agreement with the observed ones.

In addition, a comparison between the new model and the electrostatic three-center model proposed in a previous paper is discussed in brief.     

A new look at the reduced-gradient-following path

 The mathematical structure of the reduced-gradient-following (RGF) path introduced by Quapp et al. (1988 J. Comput. Chem. 19:1087) is reviewed and analyzed. We report two new algorithms to evaluate the RGF path. The RGF path is also compared mathematically and computationally with the gradient extremals path. An example of the evaluation of the RGF path is also reported. Received: 21 May 2001 / Accepted: 27 September 2001 / Published online: 9 January 2002     

Hydrogen bonds, improper hydrogen bonds and dihydrogen bonds

The structures, interaction energies and vibrational spectra of a large number of molecular complexes, formed by binary combination of the covalent hydrides of some of the elements of the first two rows of the periodic table, have been determined by means of ab initio molecular orbital theory at the MP2 level, using the 6-311++G(d,p) basis set. The results are discussed in terms of a variety of different types of interaction experienced by the monomer species as they undergo association, namely conventional hydrogen bonding, improper hydrogen bonding, dihydrogen bonding and electron donor–acceptor interaction.     

Hydrogen bonding in phenols—XI : Intramolecular hydrogen bonds in 2-hydroxy-R′-diphenylmethanes

The ν(OH) bands of a series of 2-hydroxy-R′-diphenylmethanes (R′ = H, 4′-Me, 4′-Et, 4′-CH(Me₂), 4′-C(Me₃), 2′,4′,6′-three Me, 2′,3′,5′,6′-tetra Me and 2′,3′,4′,5′,6′-penta Me) have been studied over a range of temperatures. Enthalpies (ΔH°) and entropies (ΔS°) of interaction were estimated from the temperature dependencies of equilibrium constants. The positive values of ΔH° were found with compounds containing a Me group in ortho-positions suggesting that π-associated conformers are less favoured than the free conformers.     

Photochemical oxidative addition of B-H bonds at ruthenium and rhodium

Metal phosphine hydrides of type RuP(4)H(2) and RhP(3)H(3) react photochemically with HB(pin)(pin = pinacolate) to form metal boryl hydride complexes via 16-electron intermediates generated by H(2) loss; the second order rate constants for reaction of the intermediates with HB(pin) are even larger than those for reaction with Et(3)SiH.     

The behavior of transition metal nitrido bonds towards protonation rationalized by means of localized bonding schemes and their weights

A new computational scheme is applied to rationalize the different protonation behaviors of the nitrido complexes [L'Mn(V)(N)(acac)](+), [LCr(V)(N)(acac)](+), and [LV(V)(N)(acac)](+). L and L' represent the macrocycles 1,4,7-triazacyclononane and its N-methylated derivative, respectively, and acac is the bidentate monoanion pentane-2,4-dionate. The bonds of the complexes are partitioned into bonds to be investigated and bonds of lesser interest. The investigated bonds are the transition metal nitrido bonds M(V)[triple chemical bond]N| (M = Mn, Cr, and V) and the bonds of lesser interest are located in the ligands. The ligand bonds are described by means of the strongly occupied natural bond orbitals. The electrons in the M(V)[triple chemical bond]N| nitrido bonds, however, are treated more accurately. A full configuration interaction procedure is applied in the space spanned by the strongly occupied natural bond orbitals and their corresponding antibonding orbitals. Localized bonding schemes and their weights are obtained for the d(pi)-p(pi) bonds of interest. This is achieved by representing the two-center natural bond orbitals for a d(pi)-p(pi) bond by the one-center natural hybrid orbitals localized at the bond atoms. The obtained bonding schemes are close to orthogonal valence bond structures. Their weights indicate that the nitrido nitrogen in [LV(V)(N)(acac)](+) is more easily protonated than the nitrido nitrogens in [L'Mn(V)(N)(acac)](+) and [LCr(V)(N)(acac)](+). This result is in good accord with experiment.