DFT studies of the phenol adsorption on boron nitride sheets

We perform first principles total energy calculations to investigate the atomic structures of the adsorption of phenol (C₆H₅OH) on hexagonal boron nitride (BN) sheets. Calculations are done within the density functional theory as implemented in the DMOL code. Electron-ion interactions are modeled according to the local-spin-density-approximation (LSDA) method with the Perdew-Wang parametrization. Our studies take into account the hexagonal h-BN sheets and the modified by defects d-BN sheets. The d-BN sheets are composed of one hexagon, three pentagons and three heptagons. Five different atomic structures are investigated: parallel to the sheet, perpendicular to the sheet at the B site, perpendicular to the sheet at the N site, perpendicular to the central hexagon and perpendicular to the B-N bond (bridge site). To determine the structural stability we apply the criteria of minimum energy and vibration frequency. After the structural relaxation phenol molecules adsorb on both h-BN and d-BN sheets. Results of the binding energies indicate that phenol is chemisorbed. The polarity of the system increases as a consequence of the defects presence which induces transformation from an ionic to covalent bonding. The elastic properties on the BN structure present similar behavior to those reported in the literature for graphene.     

Influence of point defects on the electronic properties of boron nitride nanosheets

Density functional theory was utilized to study the electronic properties of boron nitride (BN) sheets, taking into account the presence of defects. The structure considered consisted of a central hexagon surrounded by alternating pentagons (three) and heptagons (three). The isocoronene cluster model with an armchair edge was used with three different chemical compositions. In the first structure, three B–B bonds were formed where one B in the dimer was part of the central hexagon. In the second structure, three N–N–N bonds were formed at the periphery of the cluster, around the central hexagon. In the third structure, three N–N bonds were formed in a similar fashion to the first model. Our results indicated that the third structure was the most stable configuration; this exhibited planar geometry, semiconductor behavior, and ionic character. To explore the effects of doping, we replaced B and N atoms with C atoms, considering different atomic positions in the central hexagon. When an N atom was replaced with a C atom, the new structure was a semiconductor, but when a B atom was replaced with a C atom, the new structure was a semimetal. At the same time, the polarity increased, inducing covalent behavior. Replacing two N atoms with two C atoms also resulted in a semiconductor, while replacing two B atoms with two C atoms yielded a semimetal; in both cases the bonding was covalent. When three B (three N) atoms of the central hexagon were replaced with three C atoms, the new structure exhibited a transition to a conductor (remained a semiconductor) with low polarity. When monovacancies (N) and divacancies (B and N) were inserted into the lattice, the system was transformed into a covalent semiconductor. Finally, the electrostatic potential surface was calculated in order to explore intermolecular properties such as the charge distribution, which showed how the reactivity of the boron nitride sheets was affected by doping and orbital hybridization.     

A quantum chemical investigation of the electronic structure of thionine

We have examined the electronic and molecular structure of 3,7-diaminophenothiazin-5-ium dye (thionine) in the electronic ground state and in the lowest excited states. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction (DFT/MRCI). Equilibrium geometries were optimized employing (time-dependent) density functional theory (B3LYP functional) combined with the TZVP basis set. Solvent effects were estimated using the COSMO model and micro-hydration with up to five explicit water molecules. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet and triplet states at the ground state geometry to be of π→π* (S(1), S(2), T(1), T(2)) and n→π* (S(3), T(3)) character. This order changes when the molecular structure in the electronically excited states is relaxed. Geometry relaxation has almost no effect on the energy of the S(1) and T(1) states (~0.02 eV). The relaxation effects on the energies of S(2) and T(2) are moderate (0.14-0.20 eV). The very small emission energy results in a very low fluorescence rate. While we were not able to locate the energetic minimum of the S(3) state, we found a non-planar minimum for the T(3) state with an energy which is very close to the energy of the S(1) minimum in the gas phase (0.04 eV above). When hydration effects are taken into account, the n→π* states S(3) and T(3) are strongly blueshifted (0.33 and 0.46 eV), while the π→π* states are only slightly affected (<0.06 eV).     

Unveiling the Dynamic Processes in Hybrid Lead Bromide Perovskite Nanoparticle Thin Film Devices

Hybrid and all‐inorganic perovskite (PK) materials are a promising next generation of semiconducting materials due to their outstanding light‐harvesting features, as well as their color‐tunablility and efficient luminescent properties that lead to highly efficient photovoltaic and lighting devices. Bulk PK films are both ionic and electronic conductors under the presence of an externally applied electric field. In this work, the internal ion motion behavior is demonstrated within PK nanoparticles in thin‐film devices by means of different long‐time poling scheme assays and both static and dynamic electrochemical impedance spectroscopy measurements. In particular, the existence of a dynamic device behavior is related to the migration and rearrangement of different ionic species upon applying different driving schemes. The latter resembles the well‐known signatures of the ionic motion in light‐emitting electrochemical cells (LECs), that is, (i) the formation of electrical double layers due to the ionic distribution at the electrodes' interfaces, (ii) the growth of the doped regions once the charge injection is effective, and (iii) the subsequent formation of a non‐doped region in the bulk of the device. Hence, this comprehensive study opens up an alternative route toward understanding the dynamics inside hybrid perovskite materials based on the large body of knowledge of LECs.     

Oxygen doped SiC nanocrystals: first principles study of the optical properties

We have studied a typical spherical SiC nanocrystal with a diameter of 1.2 nm (Si₄₃C₄₄H₇₆) using linear combination of atomic orbitals in combination with pesudopotential density functional calculation. The role of fluorine and oxygen impurities was investigated on the electronic and optical properties of the Si₄₃C₄₄H₇₆ nanocrystal. Total energy calculations show that the fluorine doped Si₄₃C₄₄H₇₆ nanocrystals are unstable. Oxygen doped Si₄₃C₄₄H₇₆ have different binding energies in various substitutional and interstitial defects. The maximum binding energy of the oxygen at carbon substitutional defect is about ?0.5 eV and at interstitial defect is ?0.18 eV. The HOMO-LUMO gap of the pure Si₄₃C₄₄H₇₆ is about 6.71 eV and after doping with oxygen changes on the order of 0.1 eV. Our studies show that the refractive index of the doped Si₄₃C₄₄H₇₆ nanocrystal significantly dispersed in comparison with pure SiC nanocrystal especially at the range of 6 to 8 eV.     

Electronic sensor for sulfide dioxide based on AlN nanotubes: a computational study

Single-walled aluminum nitride nanotubes (AlNNTs) are introduced as an electronic sensor for detection of sulfur dioxide (SO(2)) molecules based on density functional theory calculations. The proposed sensor benefits from several advantages including high sensitivity: HOMO-LUMO energy gap of the AlNNT is appreciably sensitive toward the presence of SO(2) so that it decreases from 4.11?eV in the pristine tube to 1.01?eV in the SO(2)-adsorbed form, pristine application: this nanotube can detect the SO(2) molecule in its pristine type without manipulating its structure through doping, chemical functionalization, making defect, etc., short recovery time: the adsorption energy of SO(2) molecule is not so large to hinder the recovery of AlNNTs and therefore the sensor will possess short recovery times, and good selectivity: the tube can selectively detect the SO(2) molecule in the presence of several molecules such as H(2)O, CO, NH(3), HCOH, CO(2), N(2), and H(2).     

Architecture, electronic structure and stability of TM@Ge(n) (TM = Ti, Zr and Hf; n = 1-20) clusters: a density functional modeling

The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized gradient approximation. Different parameters, like, binding energy (BE), embedding energy (EE), energy gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO), ionization energy (IP), electron affinity (EA), chemical potential etc. of the energetically stable clusters (ground state cluster) in each size are calculated. From the variation of these parameters with the size of the clusters the most stable cluster within the range of calculation is identified. It is found that the clusters having 20 valence electrons turn out to be relatively more stable in both the neutral and the anionic series. The sharp drop in IP as the valence electron count increases from 20 to 21 in neutral cluster is in agreement with predictions of shell models. To study the vibrational nature of the clusters, IR and Raman spectrum of some selected TM@Ge_n (n = 15,16,17) clusters are also calculated and compared. In the end, relevance of calculated results to the design of Ge-based super-atoms is discussed.     

Scalable Water‐Based Production of Highly Conductive 2D Nanosheets with Ultrahigh Volumetric Capacitance and Rate Capability

Highly conductive and ultrathin 2D nanosheets are of importance for the development of portable electronics and electric vehicles. However, scalable production and rational design for highly electronic and ionic conductive 2D nanosheets still remain a challenge. Herein, an industrially adoptable fluid dynamic exfoliation process is reported to produce large quantities of ionic liquid (IL)‐functionalized metallic phase MoS₂ (m‐MoS₂) and defect‐free graphene (Gr) sheets. Hybrid 2D–2D layered films are also fabricated by incorporating Gr sheets into compact m‐MoS₂ films. The incorporated IL functionalities and Gr sheets prevent aggregation and restacking of the m‐MoS₂ sheets, thereby creating efficient and rapid ion and electron pathways in the hybrid films. The hybrid film with a high packing density of 2.02 g cm^?3 has an outstanding volumetric capacitance of 1430.5 F cm^?3 at 1 A g^?1 and an extremely high rate capability of 80% retention at 1000 A g^?1. The flexible supercapacitor assembled using a polymer‐gel electrolyte exhibits excellent resilience to harsh electrochemical and mechanical conditions while maintaining an impressive rate performance and long cycle life. Successful achievement of an ultrahigh volumetric energy density (1.14 W h cm^?3) using an organic electrolyte with a wide cell voltage of ≈3.5 V is demonstrated.     

Computational investigation of double nitrogen doping on graphene

Density functional theory (DFT) calculations were performed to study doping of two nitrogen atoms at different positions on a finite-sized graphene model of C₈₂H₂₄. We examined 21 structures of double nitrogen doped graphene to calculate their relative stabilities. The structure with two nitrogen atoms located apart is the most stable among the positional isomers considered in this study. For double nitrogen doping within a six-membered ring, the 1,4-position is more preferred than 1,3- or 1,2-positions for the finite-sized single layer graphene sheet. Our computational study supports the experimental observation of two nitrogen atoms at the 1,3- and 1,4-positions in a single six-membered ring of graphene. Furthermore, the structures with N-N bond are the least stable among two nitrogen doped graphene structures. The effects of nitrogen doping and the positions of two nitrogen atoms on the HOMO-LUMO energy gap of pristine graphene were analyzed.     

A comparative study on the B12N12, Al12N12, B12P12 and Al12P12 fullerene-like cages

The stability, geometry and electronic structure of the title nanoclusters were compared by using density functional theory (DFT) calculations. Their electrical property analysis showed that the relative magnitude of the HOMO-LUMO gaps (eV) that are average values from the calculated results with five different DFT functionals is as follows: B12N12(7:02)>Al12N12(4.09)>B12P12(3.80)>Al12P12(3.39). Computing the standard enthalpy and the Gibbs free energy of formation, it was found that the B(12)N(12) structure is thermodynamically stable at 298 K and 1 atmosphere of pressure, while the Al(12)N(12) structure may be stable at low temperatures. Due to positive values of change of enthalpy and entropy of formation for both the B(12)P(12) and Al(12)P(12) clusters, it seems that their formation from the consisting atoms is not spontaneous at any temperature.     

Density functional study on size-dependent structures, stabilities, electronic and magnetic properties of Au n M (M = Al and Si, n?=?1–9) clusters: comparison with pure gold clusters

The density functional theory (DFT) method has been employed to systematically investigate the geometrical structures, relative stabilities, and electronic and magnetic properties of Au(n)M (M = Al and Si, n = 1-9) clusters for clarifying the effect of Al(Si) modulation on the gold nanostructures. Of all the clusters studied, the most stable configurations adopt a three-dimensional structure for Au(n)Al at n = 4-8 and Au(n)Si at n = 3-9, while for pure gold systems, no three-dimensional lowest energy structures are obtained. Through a careful analysis of the fragmentation energy, second-order difference of energy, HOMO-LUMO energy gap, and magnetic moment as a function of cluster size, an odd-even alternative phenomenon has been observed. The results show that the clusters with even-number valence electrons have a higher relative stability, but lower magnetic moments. Furthermore, Al(Si) doping is found to enhance the stabilities of gold frameworks. In addition, the charge analysis has been given to understand the different effects of individual doped atom on electronic properties and compared further.     

First-principles study of energetic complexes (II): (5-cyanotetrazolato-N2) pentaammine cobalt (III) perchlorate (CP) and Ni, Fe and Zn analogues

First-principles methods using the TPSS density functional level of theory with the basis set 6-31G** were applied to study (5-cyanotetrazolato-N(2)) pentaammine cobalt (III) perchlorate (CP) and Ni, Fe and Zn analogues in the gas phase. The optimized lowest-energy geometry of CP was calculated from reported experimental structural data using the TPSS method. The calculated values are in good agreement with those measured by X-ray diffraction. Ni, Fe and Zn analogues were constructed and calculated on the same basis. NBO results showed that the metal-ligand interactions have covalent character. Donor-acceptor analyses predicted that the delocalization energy E(2) decreases from Co to Zn, so the covalent nature of the complexes increases in the order Co>Fe>Ni>Zn. In addition, HOMO-LUMO composition was investigated to determine the stability of the title compounds.     

Electronic structure theory based study of proline interacting with gold nano clusters

Interaction between metal nanoparticles and biomolecules is important from the view point of developing and designing biosensors. Studies on proline tagged with gold nanoclusters are reported here using density functional theory (DFT) calculations for its structural, electronic and bonding properties. Geometries of the complexes are optimized using the PBE1PBE functional and mixed basis set, i. e., 6-311++G for the amino acid and SDD for the gold clusters. Equilibrium configurations are analyzed in terms of interaction energies, molecular orbitals and charge density. The complexes associated with cluster composed of an odd number of Au atoms show higher stability. Marked decrease in the HOMO-LUMO gaps is observed on complexation. Major components of interaction between the two moieties are: the anchoring N-Au and O-Au bond; and the non covalent interactions between Au and N-H or O-H bonds. The electron affinities and vertical ionization potentials for all complexes are calculated. They show an increased value of electron affinity and ionization potential on complexation. Natural bond orbital (NBO) analysis reveals a charge transfer between the donor (proline) and acceptor (gold cluster). The results indicate that the nature of interaction between the two moieties is partially covalent. Our results will be useful for further experimental studies and may be important for future applications.     

Electronically Double‐Layered Metal Boride Hollow Nanoprism as an Excellent and Robust Water Oxidation Electrocatalysts

Metal–metalloid compounds have been paid much attention as new high‐performance water oxidation catalysts due to their exceptional durability for water oxidation in alkaline media originating from the multi‐dimensional covalent bonding of the metalloid with the surrounding metal atoms. However, compared to the excellent stability, a relatively low catalytic activity of metal‐metalloids often limits their practical application as high‐performance water oxidation catalysts. Here, for the first time, disclosed is a novel self‐templating strategy combined with atomic layer deposition (ALD) to design the electrochemically active and stable quaternary metal boride (vanadium‐doped cobalt nickel boride, VCNB), hollow nanoprism by inducing electronic double layers on the surface. The incorporation of V in a double‐layered structure can substantially increase the number of surface active sites with unsaturated electronic structure. Furthermore, the induced electronic double layers of V can effectively protect the dissolution of the surface active sites. In addition, density functional theory (DFT) calculations reveal that the impressive water oxidation properties of VCNB originate from the synergetic physicochemical effects of the different metal elements, Co and B as active sites, Ni as a surface electronic structure modifier, and V as a charge carrier transporter and supplier.     

Simulation of Adsorbate-Induced Surface Reconstruction

Abstract

Adsorbed atomic monolayers of atoms such as carbon and nitrogen can cause substantial reconstructions of a nickel {001} surface. In this simulation we combine an atomic-orbital-based calculation of electronic structure with an empirical pair-wise repulsive potential to model the covalent part of the total energy. For 0.5 monolayer coverage by the adsorbate, the surface metal layer relaxes into a p(2 × 2) structure, with transverse displacements of about 0.4 Å. At the same time these displaced surface nickel atoms ride up above second layer nickels, with a vertical displcement of about 0.4 Å. The covalent contribution to the relaxation energy comes out at about 2.0 eV per carbon atom and 1.4eV per nitrogen atom, of which the reconstruction contributes about 0.3eV.     

Photoinduced electron-transfer reaction in a ternary system involving zinc cytochrome c and plastocyanin. Interplay of monopolar and dipolar electrostatic interactions between metalloproteins.

A carbodiimide promotes noninvasive cross-linking between amino groups surrounding the exposed heme edge in zinc cytochrome c and carboxylic groups in the acidic patch in plastocyanin. Eight derivatives of the covalent complex Zncyt/pc(I), which have similar structures but different overall charges because of different numbers and locations of N-acylurea groups, are separated by cation-exchange chromatography. Kinetics of electron transfer from the diprotein complex in the triplet excited state, 3Zncyt/pc(I), to free cupriplastocyanin at pH 7.0 and various ionic strengths is studied by laser flash spectroscopy. This reaction is purely bimolecular for all eight N-acylurea derivatives of the diprotein complex. The overall charges of the derivatives 1 and 2 at pH 7.0 are -2 and 0, respectively; both of them, however, have very large dipole moments of 410-480 D. The rate constants for their reactions with cupriplastocyanin, whose charge at pH 7.0 is -8 and whose dipole moment is 362 D, are determined over the range of ionic strengths from 2.5 mM to 3.00 M. The observed dependence of the rate constants on ionic strength cannot be explained in terms of net charges (monopole-monopole interactions) alone, but it can be fitted quantitatively with a theory that recognizes also monopole-dipole and dipole-dipole interactions [van Leeuwen, J. W. (1983) Biochim. Biophys. Acta 743, 408]. At ionic strengths up to ca. 10 mM monopole-monopole interactions predominate and Br?nsted-Debye-Hückel theory applies.(ABSTRACT TRUNCATED AT 250 WORDS)     

Presence of streptococcal pyrogenic exotoxin A and C genes in human isolates of group G streptococci

The bacteriophage-associated genes speA and speC encode streptococcal pyrogenic exotoxins of group A streptococci (GAS). Human isolates of group C and G streptococci (GCS and GGS) are commensals and the closest known genetic relatives of GAS; on occasion, GCS-GGS can cause infection that is clinically similar to GAS disease. Thirty-four human isolates of GCS-GGS were tested for speA and speC. Two GGS isolates harbored speA only, whereas a third GGS had both genes. All spe alleles found in GGS were identical to known spe alleles of GAS, except for one speA allele, which was unique. The presence of shared speA and speC alleles in GAS and GGS is highly suggestive of recent interspecies transfer. Acquisition of GAS-like virulence genes by GGS may lead to enhanced pathogenicity in this usually commensal-like organism.     

The Nature of the Intramolecular Charge Transfer State in Peridinin

Experimental and theoretical evidence is presented that supports the theory that the intramolecular charge transfer (ICT) state of peridinin is an evolved state formed via excited-state bond-order reversal and solvent reorganization in polar media. The ICT state evolves in <100 fs and is characterized by a large dipole moment (∼35 D). The charge transfer character involves a shift of electron density within the polyene chain, and it does not involve participation of molecular orbitals localized in either of the β-rings. Charge is moved from the allenic side of the polyene into the furanic ring region and is accompanied by bond-order reversal in the central portion of the polyene chain. The electronic properties of the ICT state are generated via mixing of the “1¹B_u⁺” ionic state and the lowest-lying “2¹A_g^–” covalent state. The resulting ICT state is primarily ¹B_u⁺-like in character and exhibits not only a large oscillator strength but an unusually large doubly excited character. In most solvents, two populations exist in equilibrium, one with a lowest-lying ICT ionic state and a second with a lowest-lying “2¹A_g^–” covalent state. The two populations are separated by a small barrier associated with solvent relaxation and cavity formation.     

An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes

In this study, we explored the general relationship between the three-dimensional (3D) structures of enzymes and their electronic wave functions. Furthermore, we developed a method for the prediction of their functionally important sites. For this purpose, we first performed linear-scaling molecular orbital calculations for 112 nonredundant, non-homologous enzymes with known structure and function. In consequence, we showed that the canonical molecular orbitals (MOs) of the enzymes could be classified into three groups according to the degree of electron delocalization: highly localized orbitals (Group A), highly delocalized orbitals whose electrons are distributed over almost the whole molecule (Group B), and moderately delocalized orbitals (Group C). The MOs belonging to Group A are located near the HOMO-LUMO band gap, and thereby include the frontier orbitals of a given enzyme. We inferred that the MOs of Group B play a role in stabilizing the 3D structure of the enzyme, while those of Group C contribute to constructing the covalent bond framework of the enzyme. Next, we investigated whether the frontier orbitals of enzymes could be used for identifying their potential functional sites. As a result, we found that the frontier orbitals of the 112 enzymes have a high propensity to be colocalized with the known functional sites, especially when the enzymes are hydrated. Such a propensity is shown to be remarkable when Glu or Asp is a functional site residue. On the basis of these results, we finally propose a protocol for the prediction of functional sites of enzymes.     

Superantigen-like gene(s) in human pathogenic Streptococcus dysgalactiae,subsp equisimilis: genomic localisation of the gene encoding streptococcal pyrogenic exotoxin G (speG(dys))

Streptococcus pyogenes (GAS) causes about 90% of streptococcal human infections while group C (GCS) and G (GGS) streptococci can be pathogenic for different mammalians. Especially the human pathogenic GCS and GGS, Streptococcus dysgalactiae, subsp. equisimilis, account for 5-8% of the human streptococcal diseases like wound infections, otitis media, purulent pharyngitis and also streptococcal toxic shock syndrome. A defined superantigen so far was not identified in GCS and GGS strains. In the present investigation we screened DNA of GCS and GGS human isolates for the presence of genes for streptococcal pyrogenic exotoxins (spe) by hybridisation with probes that stand for the GAS genes speA, speC, speZ (smeZ), speH, speG, speI, speJ and ssa. In many GCS and GGS strains we found positive reactions with the probes speG, speJ and ssa, but not with the probes for the remaining genes under investigation. PCR amplification with subsequent sequence analysis of the PCR fragments revealed only the presence of the gene speG in GCS and GGS strains, while no DNA fragments specific for speJ and ssa could be amplified. Additionally, the upstream and downstream regions flanking speG in GGS strain 39072 were sequenced. Remarkable differences were found in the neighbourhood of speG between GAS and GGS sequences. Downstream of speG we identified in strain GGS 39072 two new open reading frames encoding proteins with no similarity to protein sequences accessible in the databases so far. In the compared GAS strains SF370 and MGAS8232, this segment, apart from some small fragments, had been deleted. Our analysis suggests that a gene transfer from GGS to GAS has preceded following deletion of the two genes orf1 and orf2 in GAS.