Electron Density Contours Research Articles

Band structure, density of states, and crystal chemistry of ZrGa2 and ZrGa3 single crystals

Using FP-LAPW Method we have performed calculations of the band structure of the ZrGa2 and ZrGa3 crystals. The all-electron full potential linearized augmented plane wave method was used to solve the Kohn Sham DFT equations. We have explored different approximations using three kinds of exchange-correlation potentials on the electronic structure and we concluded that there is insignificant influence on the band structure and the density of states. It is clear that there exists a difference in the band dispersion with one move from ZrGa2 to ZrGa3 that is attributed to the fact that ZrGa2 has four formula per unit cell (Z=4) while ZrGa3 has two formula per unit cell (Z=2). Despite some similarity in the crystallochemistry of ZrGa2 to ZrGa3 some differences are observed in the band structure dispersion. There is a strong hybridization between the states. The interaction of charges between Zr and Ga atoms is due to the strong hybridization, and the covalent bond arises due to the degree of hybridization. Hence, there is a strong covalent bonding between these atoms. We have obtained a space electron charge density distribution in the average unit cell by calculations of the electron charge density distribution. The space electronic charge density contour distribution is illustrated in (100) and (110) planes.

Interplay between halogen bonds and hydrogen bonds in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes

The character of the cooperativity between the HOX···OH/SH halogen bond (XB) and the Y-H···(H)OX hydrogen bond (HB) in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes has been investigated by means of second-order Møller-Plesset perturbation theory (MP2) calculations and "quantum theory of atoms in molecules" (QTAIM) studies. The geometries of the complexes have been determined from the most negative electrostatic potentials (V (S,min)) and the most positive electrostatic potentials (V (S,max)) on the electron density contours of the individual species. The greater the V (S,max) values of HY, the larger the interaction energies of halogen-bonded HOX···OH/SH in the termolecular complexes, indicating that the ability of cooperative effect of hydrogen bond on halogen bond are determined by V (S,max) of HY. The interaction energies, binding distances, infrared vibrational frequencies, and electron densities ρ at the BCPs of the hydrogen bonds and halogen bonds prove that there is positive cooperativity between these bonds. The potentiation of hydrogen bonds on halogen bonds is greater than that of halogen bonds on hydrogen bonds. QTAIM studies have shown that the halogen bonds and hydrogen bonds are closed-shell noncovalent interactions, and both have greater electrostatic character in the termolecular species compared with the bimolecular species.

Hypokinetic stress and neuronal porosome complex in the rat brain: The electron microscopic study

Porosomes are the universal secretory machinery in cells, where membrane-bound secretory vesicles transiently dock and fuse to release intravesicular contents to the outside of the cell during cell secretion. Studies using atomic force microscopy, electron microscopy, electron density and 3D contour mapping, provided rich nanoscale information on the structure and assembly of proteins within the neuronal porosome complex in normal brain. However it remains uncertain whether pathological conditions that alter process of neurotransmission, provoke alterations in the porosome structure also. To determine if porosomes are altered in disease states, the current study was undertaken for first time using high resolution electron microscope. One of pathologies that produce subtle alteration at the presynaptic terminals has been demonstrated to be hypokinetic stress. The central nucleus of amygdale is the brain region, where such alterations are mostly expressed. We have examined the width and depth of the neuronal porosome complex and their alterations provoked by chronic hypokinetic stress in above mentioned limbic region. Specifically, we have demonstrated that despite alterations in the presynaptic terminals and synaptic transmission provoked by this pathological condition in this region, the final step/structure in neurosecretion – the porosome – remains unaffected: the morphometric analysis of the depth and diameter of this cup-shaped structure at the presynaptic membrane point out to the heterogeneity of porosome dimensions, but with unchanged fluctuation in norm and pathology.

Electronic structure and magneto-optic Kerr effect in ferromagnetic titanium oxyphosphates Li0.50Co0.25TiO(PO4): An ab-initio study

The X-ray diffraction for Li0.50Co0.25TiO(PO4), was used as a starting point to perform structural optimization by minimizing the forces acting on the atoms. We have performed a comprehensive theoretical study of electronic properties, including magneto-optic Kerr effect, of titanium oxyphosphates Li0.50Co0.25TiO(PO4) in the ferromagnetic phase. The generalized gradient approximation (GGA) exchange-correlation potential was applied within the full potential linear augmented plane wave (FP-LAPW) method. The total energy of the ferromagnetic state is 0.72eV less than that of the paramagnetic state. The total moment is found to be 2.99μB with a major contribution of 2.47μB coming from the Co atoms. In addition, we have calculated the total and partial densities of states. The electron charge densities and the bonding properties are analyzed and discussed. As a remarkable finding we note that the ferromagnetic Li0.50Co0.25TiO(PO4), is semiconducting with energy gap of about 1.2eV for the minority spin and as semi-metallic for the majority spin, in contrast to the paramagnetic Li0.50Co0.25TiO(PO4) which shows metallic behavior. From the calculated results of band structure and density of states, the half-metallic character and stability of ferromagnetic state for Li0.50Co0.25TiO(PO4) is determined. The bonding properties of the ferromagnatic Li0.50Co0.25TiO(PO4) have been analyzed through the electronic spin charge density contours in the (100) and (110) planes. The Kerr rotation spectrum is controlled by σ2xy(ω) at low energies (1.5–3.0eV) because σ1xx(ω) is almost constant. The value of the Kerr rotation is close to 0.1 degree at low energies.

Neuronal porosome in the rat and cat brain

It is well established that during cell secretion, membrane-bound secretory vesicles dock and fuse at the base of supramolecular cup-shaped structures at the cell plasma membrane called "porosomes", to expel intra-vesicular contents to the outside. In neurons, it has been demonstrated that 12-17 nm cup-shaped lipoprotein structure possessing a central plug are present at the presynaptic membrane, where 50 nm in diameter synaptic vesicles transiently dock and fuse to release neurotransmitter. In the past decade, the neuronal porosome has been isolated and its major chemical composition determined. Additionally, the porosome has been both structurally and functionally reconstituted into artificial lipid membrane, establishing its role as the secretory portal in neurons. Studies utilizing atomic force and electron microscopy, combined with electron density and 3D contour mapping, provide at the nanoscale, the structure and assembly of proteins within the neuronal porosome. In the current study, ultrahigh resolution imaging of the presynaptic membrane of isolated brains from both rats and cats, demonstrate for the first time, the presence of neuronal porosomes in cat brain, and further confirms the presence of porosomes at the presynaptic membrane in rat brain synaptosomes. Results from the present study further confirm the cup-shaped morphology of porosomes in the rat brain, and demonstrates their similar shape and size in the cat nerve terminal. The study also demonstrates for the first time, the universal presence of similar porosomes in different species of mammals.

A Theoretical Estimation of the Charge Density Distribution in the Diluted Magnetic Semiconductors of Si<sub>1-x</sub>M<sub>x</sub> and Ge<sub>1-x</sub>M<sub>x </sub>(M = V, Mn, Co)

An effort has been made to understand the charge density distribution of the Si and Ge based diluted magnetic semiconductors. A theoretical analysis has been done on the variation of charge densities when the semiconductors Si and Ge are doped with the transition metal atoms of V, Mn and Co with different concentrations of x (0.02, 0.04, 0.06, 0.08, and 0.10), in Si1-xMx and Ge1-xMx. Two dimensional electron density contour maps have been plotted for all the compositions studied in this work. The theoretical mid bond densities were found out for the compounds which can be taken as the reference values for comparison of the experimental values of the same compositions.

Structural properties and bonding nature of 3-methyl-4-phenyl-5-(2-pyridyl)-1,2,4-triazole single crystal

The atomic positions of 3-methyl-4-phenyl-5-(2-pyridyl)-1,2,4-triazole single crystal taken from the X-ray diffraction data obtained by Liu et al. [1] were optimized by minimization of the forces acting on the atoms using a full potential linear augmented plane wave method within density-functional theory. The local density approximation (LDA) by Ceperley–Alder (CA) exchange–correlation potential was applied. The full potential calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Γ point of the Brillouin zone resulting in a direct energy gap of 3.4 eV for the original experimental structure and 3.2 eV for the optimized structure. The upper VB is formed mainly by C, H, and N atoms while the lower CB has mainly C and H atoms. We present an analysis of the partial densities of states which gives useful information on hybridization and the orbital character of the states. We have calculated the bond lengths and angles, a good agreement with the experimental data were found. The origin of the chemical bonding and the electronic charge density contour in the (1 0 0) and (1 1 0) planes were analyzed.

Electronic structure, chemical bonding features, and electron charge density of the double-cubane single crystal [Sb7S8Br2](AlCl4)3

The present calculations were performed using all-electron full potential linearized augmented plane wave method based on the density functional theory. We have optimized the structure of the double-cubane single crystal [Sb7S8Br2](AlCl4)3, starting with the x-ray diffraction data Zhang et al., [J. Am. Chem. Soc. 131, 9896 (2009)], by minimization of the forces (1 mRy/au) acting on the atoms, keeping the lattice parameters fixed at the experimental values. Our calculations show that [Sb7S8Br2](AlCl4)3 possesses a wide indirect energy band gap of about 1.6 eV (2.03 eV) using local density approximation (Engel–Vosko generalized gradient approximation) exchange correlation potentials. To describe the bonding properties we have evaluated the electronic charge space density contour in four planes-namely (001), (110), (100), and (010) which show that this compound possesses a considerable anisotropy. The contour plot shows partial ionic and strong covalent bonding between S–Sb, Al–Cl, S–Br, S–S, Cl–Cl, and Sb–Br atoms.

Density Functional Calculations, Electronic Structure, and Optical Properties of Molybdenum Bimetallic Nitrides Pt2Mo3N and Pd2Mo3N

The electronic band structure, origin of chemical bonds, and dispersion of linear optical susceptibilities for Pt(2)Mo(3)N and Pd(2)Mo(3)N have been investigated within the framework of density functional theory (DFT). The atomic positions of Pt(2)Mo(3)N and Pd(2)Mo(3)N crystalline compounds taken from the X-ray diffraction data (El-Himri, A.; Marrero-Lopez, D.; Nunez, P. J. Solid State Chem. 2004, 177, 3219) were optimized by minimization of the forces acting on the atoms using a full potential linear augmented plane wave (FLAPW) method. We employed the generalized gradient approximation (GGA) of Perdew, Burke, and Ernzerhof (PBE). The DFT calculations show that these compounds have metallic origin with strong orbital hybridization near the Fermi energy level (E(F)). The calculated density of states (DOS) at the Fermi energy (E(F)) is about 1.83 and 1.02 states/Ry cell, and the bare linear low-temperature electronic specific heat coefficient (γ) is found to be 0.32 and 0.18 mJ/mol-K(2) for Pt(2)Mo(3)N and Pd(2)Mo(3)N, respectively. The Fermi surface of Pt(2)Mo(3)N (Pd(2)Mo(3)N) is composed of three (five) sheets. The bonding features of the compounds are analyzed using the electronic charge density contour in the (110) crystallographic plane. The linear optical properties are calculated with and without the Drude term.

First-principles calculations of novel sillenite compounds Bi24M2O40 (M=Se or Te)

The electronic structures of novel sillenite compounds Bi24M2O40 (M=Se or Te) were studied by first-principles calculations. The PDOS and the band decomposed electron density contour maps projected on symmetric tetrahedral MO4 show that the novel band at the Fermi level is resulted from the antibonding interaction of cationic ns states and anionic O 2p states. Further interaction between this antibonding state and the cationic np states forms asymmetric electron densities around cation under distorted coordination. The novel band at Fermi level and the asymmetric electron densities of these two kinds of sillenite compounds may be advantageous for photocatalytic applications.

Sensitivity and the available free space per molecule in the unit cell

Invoking the known link between impact sensitivity and compressibility, we have expanded upon an earlier preliminary study of the significance of the available free space per molecule in the unit cell, ΔV. We express ΔV as V(eff) - V(int), where V(eff) corresponds to zero free space, V(eff) = molecular mass/density. V(int) is the intrinsic gas phase molecular volume. We demonstrate that V(int) can be appropriately defined as the volume enclosed by the 0.003 au contour of the molecule's electronic density; this produces packing coefficients that have the range and average value found crystallographically. Measured impact sensitivities show an overall tendency to increase as ΔV becomes larger. For nitramines, the dependence upon ΔV is rather weak; we interpret this as indicating that a single overriding factor dominates their initiation mechanism, e.g., N-NO(2) rupture. (An analogous situation appears to hold for many organic azides.) In addition to the conceptual significance of identifying ΔV as a factor in impact sensitivity, the present results allow rough estimates of relative sensitivities that are not known.

Cover Picture: Contrib. Plasma Phys. 10/2010

Abstract“Gesamtstrahlung des stationären und impulsüberlagerten Argon‐Hochtemperaturbogens” (Total emission of a stationary, current driven, high temperature argon arc). Photographs of a 10 mm long, stationary arc IB = 160A a), with superimposed current drive by means of a capacitor discharge having a voltage of 3 kV b), 3.5 kV c), and 5kV d). The exposure time was about 1/200 s. The characteristic tracer of particles emitted from the electrodes are clearly visible in the case of current drive. [Figure 3(a‐d) of the paper by Werner Neumann, Contrib. Plasma Phys. 1, 107–118 (1960).]Magnetohydrodynamic simulation of a tungsten wire ablating in a wire‐array Z pinch. Comparisons of simulation (GORGON code) and experiment at t = 200 ns: 2D contours of electron density. [Figure 4a of the paper by D.‐K. Kim et al., Contrib. Plasma Phys. 50, 115–120 (2010).]

Conformation states of the neuronal porosome complex

Porosomes are the universal secretory machinery of the cell plasma membrane, where membrane-bound secretory vesicles transiently dock and fuse to expel intravesicular contents to the environment during cell secretion. In neurons, 12- to 17-nm cup-shaped lipoprotein structures possessing a central plug are present at the presynaptic membrane, where 40-50 nm in diameter synaptic vesicles transiently dock and fuse to release neurotransmitters. The neuronal porosome complex has been isolated, its composition determined and it has been both structurally and functionally reconstituted in artificial lipid membranes. Earlier studies using AFM (atomic force microscopy), EM (electron microscopy), electron density and 3D contour mapping provide the structure and assembly of proteins within the neuronal porosome complex at the nanoscale level. A set of eight protein units lining the neuronal porosome cup is present, each connected via spoke-like elements to a central plug, hypothesized for the rapid opening and closing of the structure to the outside. In the present study, ultrahigh-resolution imaging of the presynaptic membrane of isolated synaptosome preparations demonstrate, for the first time, the presence of neuronal porosomes in both their open and close conformations. The results suggests that the central plug is retracted into the porosome cup in its open conformation and pushed outward to seal the porosome opening, supporting the hypothesis that it operates as the opening-closing device of the complex.

Satellite traces, range spread-F occurrence, and gravity wave propagation at the southern anomaly crest

Abstract. Range spread-F (RSF) and occurrence of "satellite" traces prior to RSF onset were studied at the southern peak of the ionospheric equatorial anomaly (EA). Ionograms recorded in September 2007 at the new ionospheric station of Tucumán, Argentina (26.9° S, 294.6° E, dip latitude 15.5° S), by the Advanced Ionospheric Sounder (AIS) developed at the Istituto Nazionale di Geofisica e Vulcanologia (INGV), were considered. Satellite traces (STs) are confirmed to be a necessary precursor to the appearance of an RSF trace on the ionograms. Moreover, an analysis of isoheight contours of electron density seems to suggest a relationship between RSF occurrence and gravity wave (GW) propagation.

Ab initio calculations on the structure and properties of hexagonal boron nitrides

Ab initio calculations were performed on stacked hexagonal boron nitride ( h-BN) rings, (B 3N 3) n [ n = 1–10]. These species were investigated using Hartree–Fock, Møller–Plesset second-order perturbation theory and density-functional theory methods with the 6–31 G( d) basis set. Geometry optimizations were performed followed by frequency calculations. These structures are stable using gas phase molecular orbital theory and are extremely high in energy. Semiconducting behavior was not found as determined through quantum mechanical calculations. Estimates of bond dissociation energies between rings were found to be ∼700 kJ mol −1. Electron density contour plots elucidate bonding patterns where some p-like character is mixed and covalent bonding is overwhelmingly observed.

Do the atoms at second layer block the path of vacancies in the bulk? - The DFT study of vacancies below the Mg (0001) surface

The formation energy of monovacancy and binding energy of divacancy at and below Mg (0001) surface are examined by ab initio calculations based on the density-functional theory. Appropriate dense of k-point mesh and large supercell is used to obtain reasonable values. During calculation, we find that higher formation energy is needed to form monovacancy at the second layer. The electron density contour plots shows that electron tends to accumulate in the vicinity of vacancy at the second layer and accumulation charges are also impact on the stableness of the divacancies located at different layers. The migration barrier energy of transition state for the vacancy at the second layer is counted to be very low because of the accumulation electrons apply the power to make the vacancy to migrate. Perhaps, our computational results will be useful to account for the diffusion of hydrogen atoms at bulk of Mg and the mechanism of catalysis of impurities like carbon for the diffusion of hydrogen atoms.

A possible crystal volume factor in the impact sensitivities of some energetic compounds

We have investigated the possibility of a link between the impact sensitivities of energetic compounds and the space available to their molecules in their crystal lattices. As a measure of this space, we use Delta V=V(eff)-V(0.002), where V(eff) is the effective molecular volume obtained from the crystal density and V(0.002) is that enclosed by the 0.002 au contour of the molecule's gas phase electronic density, determined computationally. When experimental impact sensitivity was plotted against Delta V for a series of 20 compounds, the nitramines formed a separate group showing little dependence upon Delta V. Their impact sensitivities correlate well with an anomalous imbalance in the electrostatic potentials on their molecular surfaces, which is characteristic of energetic compounds in general. The imbalance is symptomatic of the weakness of the N-NO(2) bonds, caused by depletion of electronic charge. The impact sensitivities of non-nitramines, on the other hand, depend much more strongly upon Delta V, and can be quite effectively related to it if an electrostatically-based correction term is included.

Laterally Extended Spiral Graphite Analogue Boron−Nitrogen Helices

Ab initio self-consistent field molecular orbital and density functional theory calculations have been performed on a series of extended helical boron-nitrogen analogues of a "spiral graphite", the [N]polymethylenylnaphthalenes (N = 6, 8, and 12), with the molecular formula N(x)B(y)H(z) (where x = 28, 37, and 55, y = 27, 36, and 54, z = 23, 29, and 41). Interchanging the positions of the boron and nitrogen atoms in the helix leads to very similar structures N(x-1)B(y+1)H(z) in all three studied cases. The electronic structure and the optimum geometries of these helices were investigated at the HF/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory. Electron density contours were calculated for the largest helices at the B3LYP/6-31G(d,p) level of theory.

Nanoscale 3D contour map of protein assembly within the astrocyte porosome complex.

The astrocyte porosome complex, the secretory machinery at the plasma membrane of astrocytes, is a 10-15 nm cup-shaped lipoprotein structure possessing a central plug. Since the porosome is a membrane-associated, multi-protein complex, it has precluded the generation of 3D crystals for X-ray diffraction studies, nor structural analysis at the atomic level using the solution NMR. These limitations were partially overcome in the current studies, furthering our understanding of the porosome structure in astrocytes. Using atomic force microscopy, electron microscopy, and electron density and 3D contour mapping, finally provides at the nanoscale, the structure and assembly of proteins within the astrocyte porosome complex. Results from this study demonstrate a set of protein units lining the porosome cup, each connected via spoke-like elements to a central plug region within the structure. In contrast to the neuronal porosome, which possess eight globular proteins at the outer rim of the complex, the porosome complex appear to possess 12 such globular structures. Nature has designed the porosome as the universal secretory machinery, but has fine-tuned its use to suite secretion from different cell types. The isolation of intact astrocyte porosomes for near-atomic resolution using cryo-electron diffraction measurements, is finally possible.

EM 3D contour maps provide protein assembly at the nanoscale within the neuronal porosome complex.

The neuronal porosome complex, the secretory machinery at the plasma membrane of nerve terminals, is a 12-17-nm cup-shaped lipoprotein structure possessing a central plug. Since the porosome is a membrane associated, multi-protein complex measuring >650 kD, it has precluded generation of 3D crystals for x-ray diffraction studies, nor structural analysis at the atomic level using solution magnetic resonance spectroscopy. These limitations were partially overcome in the current studies, furthering our understanding of the porosome structure. Using atomic force microscopy, electron microscopy and electron density and 3D contour mapping, finally provides at the nanoscale, the structure and assembly of proteins within the neuronal porosome complex. Results from this study demonstrate a set of eight protein units lining the porosome cup, each connected via spoke-like elements to a central plug region within the structure. The isolation of intact porosomes for near-atomic resolution using cryo-electron diffraction measurements, is finally possible.