Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Experimental validation of `pnicogen bonding' in nitrogen by charge density analysis

The participation of a nitrogen atom acting as an electrophile in pnicogen bonding, a hitherto unexplored interaction has been established by experimental charge density analysis. QTAIM and NBO analyses ratify this observation.

Halogen Bonding and Chalcogen Bonding in 4,7-Dibromo-5, 6-dinitro-2,1,3-benzothiadiazole

An organic solid, 4,7-dibromo-5,6-dinitro-2,1,3-benzothiadiazole, has been designed to serve as an illustrative example to quantitatively evaluate the relative merits of halogen and chalcogen bonding in terms of charge density features. The compound displays two polymorphic modifications, one crystallizing in a non-centrosymmetric space group (Z' = 1) and the other in a centrosymmetric space group with two molecules in the asymmetric unit (Z' = 2). Topological analysis based on QTAIM clearly brings out the dominance of the chalcogen bond over the halogen bond along with an indication that halogen bonds are more directional compared to chalcogen bonds. The cohesive energies calculated with the absence of both strong and weak hydrogen bonds as well as stacking interaction are indicative of the stabilities associated with the polymorphic forms.

S center dot center dot center dot O chalcogen bonding in sulfa drugs: insights from multipole charge density and X-ray wavefunction of acetazolamide

Experimental charge density analysis combined with the quantum crystallographic technique of X-ray wavefunction refinement (XWR) provides quantitative insights into the intra-and intermolecular interactions formed by acetazolamide, a diuretic drug. Firstly, the analysis of charge density topology at the intermolecular level shows the presence of exceptionally strong interaction motifs such as a DDAA-AADD (D-donor, A-acceptor) type quadruple hydrogen bond motif and a sulfonamide dimer synthon. The nature and strength of intra-molecular S center dot center dot center dot O chalcogen bonding have been characterized using descriptors from the multipole model (MM) and XWR. Although pure geometrical criteria suggest the possibility of two intra-molecular S center dot center dot center dot O chalcogen bonded ring motifs, only one of them satisfies the ``orbital geometry'' so as to exhibit an interaction in terms of an electron density bond path and a bond critical point. The presence of `s-holes' on the sulfur atom leading to the S center dot center dot center dot O chalcogen bond has been visualized on the electrostatic potential surface and Laplacian isosurfaces close to the `reactive surface'. The electron localizability indicator (ELI) and Roby bond orders derived from the `experimental wave function' provide insights into the nature of S center dot center dot center dot O chalcogen bonding.

Non-covalent C-Cl center dot center dot center dot pi interaction in acetylene-carbon tetrachloride adducts: Matrix isolation infrared and ab initio computational studies

Non-covalent halogen-bonding interactions between n cloud of acetylene (C2H2) and chlorine atom of carbon tetrachloride (CCl4) have been investigated using matrix isolation infrared spectroscopy and quantum chemical computations. The structure and the energies of the 1:1 C2H2-CCl4 adducts were computed at the B3LYP, MP2 and M05-2X levels of theory using 6-311++G(d,p) basis set. The computations indicated two minima for the 1:1 C2H2-CCl4 adducts; with the C-Cl center dot center dot center dot pi adduct being the global minimum, where pi cloud of C2H2 is the electron donor. The second minimum corresponded to a C-H...Cl adduct, in which C2H2 is the proton donor. The interaction energies for the adducts A and B were found to be nearly identical. Experimentally, both C-Cl center dot center dot center dot pi and C-H center dot center dot center dot Cl adducts were generated in Ar and N2 matrixes and characterized using infrared spectroscopy. This is the first report on halogen bonded adduct, stabilized through C-Cl center dot center dot center dot pi interaction being identified at low temperatures using matrix isolation infrared spectroscopy. Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were performed to support the experimental results. The structures of 2:1 ((C2H2)(2)-CCl4) and 1:2 (C2H2-(CCl4)(2)) multimers and their identification in the low temperature matrixes were also discussed. (C) 2015 Elsevier B.V. All rights reserved.

Organization dependent collective magnetic properties of secondary nanostructures with differential spatial ordering and magnetic easy axis orientation

Achieving control on the formation of different organization states of magnetic nanoparticles is crucial to harness their organization dependent physical properties in desired ways. In this study, three organization states of iron oxide nanoparticles (gamma-Fe2O3), defining as (i) assembly (ii) network aggregate and (iii) cluster, have been developed by simply changing the solvent evaporation conditions. All three systems have retained the same phase and polydispersity of primary particles. Magnetic measurements show that the partial alignment of the easy axes of the particles in the network system due to the stacking aggregation morphology can result in significant enhancement of the coercivity and remanence values, while the opposite is obtained for the cluster system due to the random orientation of easy axes. Partial alignment in the aggregate system also results in noticeable non -monotonic field dependence of ZFC peak temperature (TpeaB). The lowest value of the blocking temperature (TB) for the cluster system is related to the lowering of the effective anisotropy due to the strongest demagnetizing effect. FC (Field cooled) memory effect was observed to be decreasing with the increasing strength of dipolar interaction of organization states. Therefore, the stacking aggregation and the cluster formation are two interesting ways of magnetic nanoparticles organization for modulating collective magnetic properties significantly, which can have renewed application potentials from recording devices to biomedicine. (C) 2016 Elsevier B.V. All rights reserved.

Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding.

We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO(2) polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress, and interactions with single water molecules of a natively oxidized Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidized and amorphous silica surfaces of 97 and 90 mJm(2), respectively, at a water adsorption coverage of approximately 1 ML. The difference arises from the stronger interaction of the natively oxidized surface with liquid water, resulting in a higher heat of immersion (203 vs 166 mJm(2)), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller densities with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account.

Heating characteristics of blunt swept fin-induced shock wave turbulent boundary layer interaction

An experimental study was conducted on shock wave turbulent boundary layer interactions caused by a blunt swept fin-plate configuration at Mach numbers of 5.0, 7.8, 9.9 for a Reynolds number range of (1.0.similar to 4.7) x 10(7)/m. Detailed heat transfer and pressure distributions were measured at fin deflection angles of up to 30 degrees for a sweepback angle of 67.6 degrees. Surface oil flow patterns and liquid crystal thermograms as well as schlieren pictures of fin shock shape were taken. The study shows that the flow was separated at deflection of 10 degrees and secondary separation were detected at deflection of theta greater than or equal to 20 degrees. The heat transfer and pressure distributions on flat plate showed an extensive plateau region followed by a distinct dip and local peak close to the fin foot. Measurements of the plateau pressure and heat transfer were in good agreement with existing prediction methods, but pressure and heating peak measurements at M greater than or equal to 6 were significantly lower than predicted by the simple prediction techniques at lower Mach numbers.

Quantum Monte Carlo study of the CO interaction with a dimer model surface for Cr(110)

The chemisorption of CO on a Cr( 110) surface is investigated using the quantum Monte Carlo method in the diffusion Monte Carlo (DMC) variant and a model Cr2CO cluster. The present results are consistent with the earlier ab initio HF study with this model that showed the tilted/ near-parallel orientation as energetically favoured over the perpendicular arrangement. The DMC energy difference between the two orientations is larger (1.9 eV) than that computed in the previous study. The distribution and reorganization of electrons during CO adsorption on the model surface are analysed using the topological electron localization function method that yields electron populations, charge transfer and clear insight on the chemical bonding that occurs with CO adsorption and dissociation on the model surface.

Influence of secondary void damage in the matrix material around voids

The mechanism of ductile damage caused by secondary void damage in the matrix around primary voids is studied by large strain, finite element analysis. A cylinder embedding an initially spherical void, a plane stress cell with a circular void and plane strain cell with a cylindrical or a flat void are analysed under different loading conditions. Secondary voids of smaller scale size nucleate in the strain hardening matrix, according to the requirements of some stress/strain criteria. Their growth and coalescence, handled by the empty element technique, demonstrate distinct mechanisms of damage as circumstances change. The macroscopic stress-strain curves are decomposed and illustrated in the form of the deviatoric and the volumetric parts. Concerning the stress response and the void growth prediction, comparisons are made between the present numerical results and those of previous authors. It is shown that loading condition, void growth history and void shape effect incorporated with the interaction between two generations of voids should be accounted for besides the void volume fraction.

Bonding regimes of nitrogen in amorphous carbon

Nitrogen can have numerous effects on diamond-like carbon: it can dope, it can form the hypothetical superhard compound C3N4, or it can create fullerene-like bonding structures. We studied amorphous carbon nitrogen films deposited by a filtered cathodic vacuum arc as a function of nitrogen content, ion energy and deposition temperature. The incorporation of nitrogen from 10-2 to 10 at% was measured by secondary ion mass spectrometry and elastic recoil detection analysis and was found to vary slightly sublinearly with N2 partial pressure during deposition. In the doping regime from 0 to about 0.4% N, the conductivity changes while the sp3 content and optical gap remain constant. From 0.4 to approximately 10% N, existing sp2 sites condense into clusters and reduce the band gap. Nitrogen contents over 10% change the bonding from mainly sp3 to mainly sp2. Ion energies between 20 and 250 eV do not greatly modify this behaviour. Deposition at higher temperatures causes a sudden loss of sp3 bonding above about 150 °C. Raman spectroscopy and optical gap data show that existing sp2 sites begin to cluster below this temperature, and the clustering continues above this temperature. This transition is found to vary only weakly with nitrogen addition, for N contents below 10%.

A novel short neurotoxin, cobrotoxin c, from monocellate cobra (Naja kaouthia) venom: isolation and purification, primary and secondary structure determination, and tertiary structure modeling

A novel short neurotoxin, cobrotoxin c (CBT C) was isolated from the venom of monocellate cobra (Naja kaouthia) using a combination of ion-exchange chromatography and FPLC. Its primary structure was determined by Edman degradation. CBT C is composed of 61 amino acid residues. It differs from cobrotoxin b (CBT B) by only two amino acid substitutions, Thr/Ala11 and Arg/Thr56, which are not located on the functionally important regions by sequence similarity. However, the LD50 is 0.08 mg/g to mice, i.e. approximately five-fold higher than for CBT B. Strikingly, a structure-function relationship analysis suggests the existence of a functionally important domain on the outside of Loop III of CBT C. The functionally important basic residues on the outside of Loop III might have a pairwise interaction with alpha subunit, instead of gamma or delta subunits of the nicotinic acetylcholine receptor (nAChR). (C) 2002 Elsevier Science Inc. All rights reserved.

Active control of normal shock wave/turbulent boundary layer interaction using "Smart" piezoelectric flap actuators

This paper looks at active control of the normal shock wave/turbulent boundary layer interaction (SBLI) using smart flap actuators. The actuators are manufactured by bonding piezoelectric material to an inert substrate to control the bleed/suction rate through a plenum chamber. The cavity provides communication of signals across the shock, allowing rapid thickening of the boundary layer approaching the shock, which splits into a series of weaker shocks forming a lambda shock foot, reducing wave drag. Active control allows optimum control of the interaction, as it would be capable of positioning the control region around the original shock position and control the rate of mass transfer. © 2004 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Interaction Between Tripeptide Gly-Gly-His and Cu2+ Probed by Microcantilevers

Gly-Gly-His tripeptide modified microcantilever was developed by carbodiimide attachment of the Gly-Gly-His tripeptide onto a 3-mercaptopropionic acid(MPA) modified gold surface. The interaction of peptide with Cu2+ ion was studied. At a relative high concentration of Cu2+, the cantilever bent toward the gold side initially as the N atom of imidazole ring and carboxyl group in different peptide coordinate with Cu2+, which results in a tensile surface stress. And then the reversed deflection of microcantilever was observed, which implies that the peptide-Cu2+ complex are formed with conformation transition. In another case, i.e., at a relative low concentration Of Cu2+, only the process of conformation transition was observed due to the coordination mode can not be formed initially. The influences of pH and salt concentration of the test solution on the performance of the sensor were studied. The results show that the maximum deflection was obtained at pH 7 and the bonding Of Cu2+ to the Gly-Gly-His tripeptide was inhibited due to the formation Of CuClx2-x.

Study of the effect of hydrogen bonding on the phase behaviour of p-nitro azobenzene derivatives with hydrophilic tails

The infrared spect ra of N-n-(4-nitrophenyl)azophenyloxyalkyldiethanolamines (Cn) are examined in the range of 4000-400 cm(-1) at different temperatures and the assignment of the fundamental vibrations given. Based on (1) the localization of the broad absorption band at 3456 cm(-1), and (2) attribution of the associated OH bands centred at 1410-1390, 1100, and 650-634 cm(-1) to, respectively delta OH deformation, nu C-O stretching and gamma OH out-of-plane bending, intermolecular hydrogen bonding between OH groups in the crystalline, liquid crystalline and isotropic states is proposed. By considering the results of FTIR, WAXD and DSC measurements, the molecular arrangement of C10 in its smectic A phase as consisting of hydrogen bonding and strong interaction between dipolar groups (NO,) is proposed. This may explain the high stability and high orientational ordering property of Cn compounds in the liquid crystalline state compared with that of n-bromo-1-[4-(4-nitrophenyl)azophenyl]oxyalkanes (Bn).