Overlapping electron density and the global delocalization of π-aromatic fragments as the reason of conductivity of the biphenylene network

Recently fabricated 2D biphenylene network is an astonishing solid-state material, which possesses unique metal-like conductive properties. At the same time, two-dimensional boron nitride network (2D-BN)—an isoelectronic and structural analogue of biphenylene network, is an insulator with a wide direct bandgap. This study investigates the relationship between the electronic properties and chemical bonding patterns for these species. It is shown that the insulating 2D-BN network possesses a strong localization of electron density on the nitrogen atoms. In turn, for a carbon-containing sheet, we found a highly delocalized electron density and an appreciable overlap of p_z orbitals of neighboring C₆ rings, which might be a reason for the conductive properties of the material.     

Topology of the electron density of multicenter bonding in the anion TCNE2 2−

For TCNE₂ ^2? the role of bond paths in the electron density is emphasized to show that the anion contains multicenter bonding interactions across 4 central carbon atoms conferring inherent stability to it, consistent with experimental, and theoretical studies of other authors.     

Fast electron density methods in the life sciences--a routine application in the future?

The understanding of mutual recognition of biologically interacting systems on an atomic scale is of paramount importance in the life sciences. Electron density distributions that can be obtained from a high resolution X-ray diffraction experiment can provide--in addition to steric information--electronic properties of the species involved in these interactions. In recent years experimental ED methods have seen several favourable developments towards successful application in the life sciences. Experimental and methodological advances have made possible on the one hand high-speed X-ray diffraction experiments, and have allowed on the other hand the quantitative derivation of bonding, non-bonding and atomic electronic properties. This has made the investigation of a large number of molecules possible, and moreover, molecules with 200 or more atoms can be subject of experimental ED studies, as has been demonstrated by the example of vitamin B12. Supported by the experimentally verified transferability concept of submolecular electronic properties, a key issue in Bader's The Quantum Theory of Atoms in Molecules, activities have emerged to establish databases for the additive generation of electron densities of macromolecules from submolecular building blocks. It follows that the major aims of any experimental electron density work in the life sciences, namely the generation of electronic information for a series of molecules in a reasonable time and the study of biological macromolecules (proteins, polynucleotides), are within reach in the near future.     

Congested molecules. Where is the steric repulsion? An analysis of the electron density by the method of interacting quantum atoms

The computed electron density of several congested saturated hydrocarbons and halogenated derivatives has been analyzed by the method of interacting quantum atoms (IQA). For all the molecules studied, the calculations show the existence of a bond path between the congested atoms and which, according to the Quantum Theory of Atoms in Molecules, indicates that there is a stabilizing interaction between these atoms. The bond path is found to exist up to interatomic distances well‐beyond the sum of the van der Waals radii. The IQA results indicate that steric hindrance is not a repulsive force between the congested atoms but that is the result of an increase in the intra‐atomic or self‐energy of the congested atoms. This increase in self‐energy is caused by the deformation of the atomic basin of the congested atoms. © 2013 Wiley Periodicals, Inc.     

Synthesis and structure of metalloid aluminum clusters—intermediates on the way to the elements

Metastable Aluminum(I) halide solutions proved to have a high potential for the synthesis of novel subvalent Al compounds, such as Al_nX_m species (X=Cl, Br, I; n<m, average oxidation state of Al below +3 or n>m, average oxidation state of Al below +1) or Al_nR_m species (R=bulky ligand; n>m). There are two principal reaction types, which are essential for the formation of the compounds discussed herein. The disproportionation, which finally results in Al(III) halides and Al metal and the metathesis which leads to a substitution of X atoms against R groups. By this way the metalloid cluster compounds [Al₇{N(SiMe₃)₂}₆]⁻, [Al₁₂{N(SiMe₃)₂}₈]⁻, [Al₁₄I₆{N(SiMe₃)₂}₆]²⁻, [Al₆₉{N(SiMe₃)₂}₁₈]³⁻, and [Al₇₇{N(SiMe₃)₂}₂₀]²⁻ could be isolated. The characteristic feature of these metalloid Al clusters is the number of AlAl contacts being larger than the number of Alligand bonds, i.e. there are more ‘naked’ than ligand-bonded Al atoms. Furthermore, the topology of the closest packing in Al metal is already pre-formed in these compounds.     

Do one-step mechanisms always involve simultaneous evolution of electron density? QTAIM/IQA analysis of the Curtius rearrangement

The Curtius rearrangement reaction is studied by using quantum theory of atoms in molecules (QTAIM) analysis of the electron density and the interacting quantum atoms (IQA) formalism. Although the rearrangements take place in one stage, two phases are distinguished when the rearranged atom is H: the first one corresponds to the separation of N₂, and the second one to the N-H/C-H bond rearrangement. The transition state (TS) for the reaction does not represent an intermediate between reagent and product for the migration but for the isolation of the N₂ molecule. When the migration is undergone by a fluorine atom, no electronic phases can be distinguished and the process is really concerted. As the migration happens closer to the TS, the TS is more similar to the product. The IQA analysis reveals different electron density evolutions for H and F migrations, and the scarce relevance (in terms of energy) of the point where BCPs appear or disappear.     

Bond Fukui functions as descriptor of the electron density reorganization in π conjugated systems

The bond Fukui function is introduced and tested as a new reactivity index capable of predicting the evolution of bond breaking and formation processes during an organic reaction involving π conjugated systems. As an illustration, we examine many cases where substituted ethylenes and dienes may respond to different reagents to yield cycloaddition, Michael addition, and other reactions at double bonds.     

Application of capillary affinity electrophoresis and density functional theory to the investigation of valinomycin–lithium complex

Capillary affinity electrophoresis (CAE) and quantum mechanical density functional theory (DFT) have been applied to the investigation of interactions of valinomycin (Val), a macrocyclic dodecadepsipeptide antibiotic ionophore, with lithium cation Li⁺. Firstly, from the dependence of effective electrophoretic mobility of Val on the Li⁺ ion concentration in the background electrolyte (BGE) (methanolic solution of 50 mM chloroacetic acid, 25 mM Tris, pH_MeOH 7.8, 0–40 mM LiCl), the apparent binding (stability) constant (K_b) of Val–Li⁺ complex in methanol was evaluated as log K_b = 1.50 ± 0.24. The employed CAE method include correction of the effective mobilities measured at ambient temperature, at different input power (Joule heating) and at variable ionic strength of the BGEs to the mobilities related to the reference temperature 25 °C and to the constant ionic strength 25 mM. Secondly, using DFT calculations, the most probable structures of the non-hydrated Val–Li⁺ and hydrated Val–Li⁺·3H₂O complex species were predicted.     

Comparison of the site occupancies determined by combined Rietveld refinement and density functional theory calculations: example of the ternary Mo-Ni-Re σ phase

The site occupancies of the Mo-Ni-Re σ phase have been studied as a function of the composition in the ternary homogeneity domain by both experimental measurements and calculations. Because of the possible simultaneous occupancy of three elements on the five sites of the crystal structure, the experimental determination of the site occupancies was achieved by using combined Rietveld refinement of X-ray and neutron diffraction data, whereas calculation of the site occupancies was carried out by using the density functional theory results of every ordered (i.e., 3(5) = 243) configuration appearing in the ternary system. A comparison of the experimental and calculation results showed good agreement, which suggests that the topologically close-packed phases, such as the σ phase, could be described by the Bragg-Williams approximation (i.e., ignoring the short-range-order contributions). On the other hand, the atomic distribution on different crystallographic sites of the Mo-Ni-Re σ phase was found to be governed by the atomic sizes. Ni, having the smallest atomic size, showed a preference for low-coordination-number (CN) sites, whereas Mo, being the largest in atomic size, preferred occupying high-CN sites. However, the preference of Re, having intermediate atomic size, varied depending on the composition, and a clear reversal in the preference of Re as a function of the composition was evidenced in both the calculated and experimental site-occupancy results.     

Paradigms and paradoxes: what are the 54 electron affinities of O2?

Only one electron affinity of oxygen, 43(1) kJ mol⁻¹ is generally cited since the molecular orbital theory anion bond order [3/4] gives an electron affinity, 14 kJ mol⁻¹. However, electron correlation rules predict 27 bonding and 27 antibonding spin orbital coupling states. The relative bond orders (RBOs), 12/13 to [1/4] and the 13 valence electrons of superoxide are used to calculate electron affinities 103 to −243 kJ mol⁻¹ consistent with experimental and theoretical values. These are used to construct 54 ionic Morse potentials.     

Comparison of LC and UPLC Coupled to MS–MS for the Determination of Sulfonamides in Egg and Honey

Determination of ten sulfonamides (SAs) in egg and honey has been compared using column liquid chromatography (LC) and ultra-performance liquid chromatography (UPLC) coupled to tandem mass spectrometry (MS–MS). A liquid–liquid extraction with acetonitrile followed by solid-phase extraction on a Strata-X cartridge was developed for sample preparation. The analytical performance of both methods was compared applying the alternative matrix-comprehensive in-house validation approach using specially designed software InterVal?. Using UPLC the separation time was shortened about 30% reducing the run time by 8 min and a better resolution was achieved compared to LC. Due to higher peak efficiency achieved with UPLC, the decision limit values obtained by both techniques were almost equal (6.61–9.43 μg kg^?1 and 7.25–11.9 μg kg^?1 for UPLC and LC, respectively), despite the fact that in UPLC twice lower sample volumes were injected. Satisfactory and comparable recoveries (80–110%) were obtained by UPLC and LC for all the SAs, except for sulfacetamide by LC and sulfabenzamide by both methods. For a majority of the spiked compounds, UPLC gave significantly better precision.     

Where does the electron go? Electron distribution and reactivity of peptide cation radicals formed by electron transfer in the gas phase

We report the first detailed analysis at correlated levels of ab initio theory of experimentally studied peptide cations undergoing charge reduction by collisional electron transfer and competitive dissociations by loss of H atoms, ammonia, and N-C alpha bond cleavage in the gas phase. Doubly protonated Gly-Lys, (GK + 2H) (2+), and Lys-Lys, (KK + 2H) (2+), are each calculated to exist as two major conformers in the gas phase. Electron transfer to conformers with an extended lysine chain triggers highly exothermic dissociation by loss of ammonia from the Gly residue, which occurs from the ground ( X ) electronic state of the cation radical. Loss of Lys ammonium H atoms is predicted to occur from the first excited ( A ) state of the charge-reduced ions. The X and A states are nearly degenerate and show extensive delocalization of unpaired electron density over spatially remote groups. This delocalization indicates that the captured electron cannot be assigned to reduce a particular charged group in the peptide cation and that superposition of remote local Rydberg-like orbitals plays a critical role in affecting the cation-radical reactivity. Electron attachment to ion conformers with carboxyl-solvated Lys ammonium groups results in spontaneous isomerization by proton-coupled electron transfer to the carboxyl group forming dihydroxymethyl radical intermediates. This directs the peptide dissociation toward NC alpha bond cleavage that can proceed by multiple mechanisms involving reversible proton migrations in the reactants or ion-molecule complexes. The experimentally observed formations of Lys z (+*) fragments from (GK + 2H) (2+) and Lys c (+) fragments from (KK + 2H) (2+) correlate with the product thermochemistry but are independent of charge distribution in the transition states for NC alpha bond cleavage. This emphasizes the role of ion-molecule complexes in affecting the charge distribution between backbone fragments produced upon electron transfer or capture.     

Exchange energy density and exchange potential via a hartree–fock plus mp2 study of the electron liquid in the ground-state conformer of glycine

Very recent criticisms of existing exchange-correlation functionals by Wanko et al. applied to systems of biological interest have led us to reopen the question of the ground-state conformer of glycine: the simplest amino acid. We immediately show that the global minimum of the Hartree–Fock (HF) ground-state leads to a planar structure of the five non-hydrogenic nuclei, in the non-ionized form NH₂–CH₂–COOH. This is shown to lie lower in energy than the zwitterion structure NHB₃ ⁺–CH₂–COO^?, as required by experiment. Refinement of the nuclear geometry using second-order Møller–Plesset perturbation theory (MP2) is also carried out, and bond lengths are found to accord satisfactorily with experimentally determined values. The ground-state electron density for the MP2 geometry is then redetermined by HF theory and equidensity contours are displayed. The HF first-order density matrix γ( r , r ′) is then used to obtain similar exchange-energy density (ε _x ( r )) contours for the lowest conformer of glycine. At first sight, their shape looks almost the same as for the density ρ( r ), which seems to vindicate the LDA proportional to ρ( r )^3/4. However, by way of an analytically soluble model for an atomic ion, it is shown that this has to be corrected to obtain an accurate HF exchange energy E_x as the volume integral of ε _x ( r ). Finally, recognizing that for larger amino acids, the use of HF plus MP2 perturbation corrections will become prohibitive, we have used the HF information for ε _x ( r ) and ρ( r ) to plot the truly non-local exchange potential proposed by Slater, from the density matrix γ( r , r ′). This latter calculation should be practicable for large amino acids, but there adopting Becke's one-parameter form of ε _x ( r ) correcting LDA exchange. Some future directions are suggested.     

A density functional study of the reactivity and stability of mixed copper complexes. Is hardness the reason?

Mixed-ligand Cu2+ ternary complexes, formed by an aromatic diimine and a second ligand with O donor atoms, show a higher than expected stability. To understand the factors affecting the stability of these systems, we performed a density functional study of [Cu(H2O)5]2+, [Cu(N-N)(H2O)3]2+, and [Cu(N-N)(O-O)H2O] (N-N is 1,10-phenanthroline, 5-nitro-1,10-phenanthroline, or 3,4,7,8-tetramethyl-1,10-phenanthroline; and O-O is oxalate). In the present study, full geometry optimization (B3LYP/3-21G**) has been performed without symmetry constraints and a comparison with some available experimental results has been made. Bond distances, equilibrium geometries, harmonic frequencies, and net atomic charges from Mulliken populations are presented. Since the principle of hard and soft acids and bases has been widely used to explain the stability of these complexes, we also calculated and analyzed the global hardness and the local softness. The results of the global hardness do not support the commonly held idea that harder acids will preferably bind to harder ligands, while softer acids will bind to softer ligands. Interestingly, local softness and electron affinity correlate well with the formation constants of these compounds and provide an explanation of the reactivity behavior. The present results may help to rationalize the stability and reactivity of these systems.     

Comparison of different mixing rules for prediction of density and residual internal energy of binary and ternary Lennard–Jones mixtures

Mixing rules are necessary when equations of state for pure fluids are used to calculate various thermodynamic properties of fluid mixtures. The well-known van der Waals one-fluid (vdW1) mixing rules are proved to be good ones and widely used in different equations of state. But vdW1 mixing rules are valid only when molecular size differences of components in a mixture are not very large. The vdW1 type density-dependent mixing rule proposed by Chen et al. [1] is superior for the prediction of pressure and vapor–liquid equilibria when components in the mixture have very different sizes. The extension of the mixing rule to chain-like molecules and heterosegment molecules was also made with good results. In this paper, the comparison of different mixing rules are carried out further for the prediction of the density and the residual internal energy for binary and ternary Lennard–Jones (LJ) mixtures with different molecular sizes and different molecular interaction energy parameters. The results show that the significant improvement for the prediction of densities is achieved with the new mixing rule [1], and that the modification of the mixing rule for the interaction energy parameter is also necessary for better prediction of the residual internal energy.     

Can a dipole-bound electron form a pseudo-atom? An atoms-in-molecules study of the hydrated electron

Non-nuclear local maxima, or attractors, of electron density are a rare but very interesting feature of the electron density distribution in molecules and solids. Recently, non-nuclear attractors (NNAs) and the corresponding pseudoatoms of electron density have been identified with the quantum theory of atoms in molecules for some anionic clusters formed by several polar solvent molecules and an excess electron bound in either a solvated-electron or dipole-bound fashion. This contribution reports a detailed study of the topology of the electron density for a series of dipole-bound water cluster anions, as calculated with Hartree-Fock, M?ller-Plesset perturbation theory, and coupled-cluster methods together with basis sets augmented with extra diffuse basis functions to accommodate the excess electron. For dipole-bound clusters, electron densities obtained with insufficient inclusion of electron correlation effects and tight basis sets feature a well-pronounced pseudoatom due to the excess electron, which ultimately disappears when a higher level of electronic structure theory and a more diffuse basis set are used. On the other hand, for solvated-electron clusters, where the excess electron is surrounded by solvent molecules, the existence of NNAs does not seem to be an artifact of the method employed, but rather a genuine feature of the electron density distribution. Pseudoatoms of electron density thus appear to be an exclusive feature of confined environments and are unlikely to be found on the tip of a cluster dipole or on solid surfaces.