Crystalline ethane-1,2-diol does not have intra-molecular hydrogen bonding: Experimental and theoretical charge density studies

The X-ray structure and electron density distribution of ethane-1,2-diol (ethylene glycol), obtained at a resolution extending to 1.00 Å−1 in sin θ/λ (data completion = 100% at 100 K) by in situ cryocrystallization technique is reported. The diol is in the gauche (g′Gt) conformation with the crystal structure stabilised by a network of inter-molecular hydrogen bonds. In addition to the well-recognized O–H···O hydrogen bonds there is topological evidence for C–H···O inter-molecular interactions. There is no experimental electron density based topological evidence for the occurrence of an intra-molecular hydrogen bond. The O···H spacing is not, vert, similar0.45 Å greater than in the gas-phase with an O–H···O angle close to 90°, calling into question the general assumption that the gauche conformation of ethane-1,2-diol is stabilised by the intra-molecular oxygen–hydrogen interaction.

Nature of Cl center dot center dot center dot Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis:Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl center dot center dot center dot Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.

Halogen Bonding in 2,5-Dichloro-1,4-benzoquinone: Insights from Experimental and Theoretical Charge Density Analysis

Experimental charge density distribution in 2, 5-dichloro-1, 4-benzoquinone has been carried out using high resolution X-ray diffraction data at 90 K to quantitatively evaluate the nature of C-Cl center dot center dot center dot O=C halogen bond in molecular crystals. Additionally, the halogen bond is studied from geometrical point of view and the same has been visualized using Hirshfeld surface analysis. The obtained results from experimental charge density analysis are compared with periodic quantum calculations using B3LYP 6-31G(d,p) level of theory. The topological values at bond critical point, three-dimensional static deformation density features and electrostatic potential isosurfaces unequivocally establish the attractive nature of C-Cl center dot center dot center dot O=C halogen bond in crystalline lattice.

Topological electron density analysis and electrostatic properties of aspirin: an experimental and theoretical study

The topological and the electrostatic properties of the aspirin drug molecule were determined from high-resolution X-ray diffraction data at 90 K, and the corresponding results are compared with the theoretical calculations. The electron density at the bond critical point of all chemical bonds induding the intermolecular interactions of aspirin has been quantitatively described using Bader's quantum theory of ``Atoms in Molecules''. The electrostatic potential of the molecule emphasizes the preferable binding sites of the drug and the interaction features of the molecule, which are crucial for drug-receptor recognition. The topological analysis of hydrogen bonds reveals the strength of intermolecular interactions.

Topological analysis of electron density and the electrostatic properties of isoniazid: an experimental and theoretical study

Isoniazid (isonicotinohydrazide) is an important first-line antitubercular drug that targets the InhA enzyme which synthesizes the critical component of the mycobacterial cell wall. An experimental charge-density analysis of isoniazid has been performed to understand its structural and electronic properties in the solid state. A high-resolution single-crystal X-ray intensity data has been collected at 90 K. An aspherical multipole refinement was carried out to explore the topological and electrostatic properties of the isoniazid molecule. The experimental results were compared with the theoretical charge-density calculations performed using CRYSTAL09 with the B3LYP/6-31G** method. A topological analysis of the electron density reveals that the Laplacian of electron density of the N-N bond is significantly less negative, which indicates that the charges at the b.c.p. (bond-critical point) of the bond are least accumulated, and so the bond is considered to be weak. As expected, a strong negative electrostatic potential region is present in the vicinity of the O1, N1 and N3 atoms, which are the reactive locations of the molecule. The C-H center dot center dot center dot N, C-H center dot center dot center dot O and N-H center dot center dot center dot N types of intermolecular hydrogen-bonding interactions stabilize the crystal structure. The topological analysis of the electron density on hydrogen bonding shows the strength of intermolecular interactions.

Density Functional Theoretical Modeling, Electrostatic Surface Potential and Surface Enhanced Raman Spectroscopic Studies on Biosynthesized Silver Nanoparticles: Observation of 400 pM Sensitivity to Explosives

Interaction of adsorbate on charged surfaces, orientation of the analyte on the surface, and surface enhancement aspects have been studied. These aspects have been explored in details to explain the surface-enhanced Raman spectroscopic (SERS) spectra of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (HNIW or CL-20), a well-known explosive, and 2,4,6-trinitrotoluene (TNT) using one-pot synthesis of silver nanoparticles via biosynthetic route using natural precursor extracts of clove and pepper. The biosynthesized silver nanoparticles (bio Ag Nps) have been characterized using UV-vis spectroscopy, scanning electron microscopy and atomic force microscopy. SERS studies conducted using bio Ag Nps on different water insoluble analytes, such as CL-20 and TNT, lead to SERS signals at concentration levels of 400 pM. The experimental findings have been corroborated with density functional computational results, electrostatic surface potential calculations, Fukui functions and potential measurements.

Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study

An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data (sin theta/lambda)(max) = 1.1 angstrom(-1)] measured at 100 (2) K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H center dot center dot center dot N and N-H center dot center dot center dot O hydrogen bonds, in which the N3-H3B center dot center dot center dot N1 and N3-H3A center dot center dot center dot O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N center dot center dot center dot H and O center dot center dot center dot H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the pi-electron cloud.

Experimental and theoretical study on numerical density evolution of short fatigue cracks

Fatigue testing was performed using a kind of triangular shaped specimen to obtain the characteristics of numerical density evolution for short cracks at the primary stage of fatigue damage. The material concerned is a structural alloy steel. The experimental results show that the numerical density of short cracks reaches the maximum value when crack length is slightly less than the average grain diameter, indicating grain boundary is the main barrier for short crack extension. Based on the experimental observations and related theory, the expressions for growth velocity and nucleation rate of short cracks have been proposed. With the solution to phase space conservation equation, the theoretical results of numerical density evolution for short cracks were obtained, which were in agreement with our experimental measurements.

Theoretical Analysis of Gain and Threshold Current Density for Long Wavelength GaAs-Based Quantum-Dot Lasers

Quantum dot gain spectra based on harmonic oscillator model are calculated including and excluding excitons. The effects of non-equilibrium distributions are considered at low temperatures. The variations of threshold current density in a wide temperature range are analyzed and the negative characteristic temperature and oscillatory characteristic temperature appearing in that temperature range are discussed. Also,the improvement of quantum dot lasers＇ performance is investigated through vertical stacking and p-type doping and the optimal dot density, which corresponds to minimal threshold current density,is calculated.

Theoretical investigation of LaC3n+ (n = 0, 1, 2) clusters by density functional theory

LaC3n+ (n = 0, 1, 2) clusters have been studied using B3LYP (Becke 3-parameter-Lee-Yang-Parr) density functional method. The basis set is Dunning/ Huzinaga valence double zeta for carbon and [2s2p2d] for lanthanum, denoted LANL1DZ. Four isomers are presented for each cluster; two of them are edge binding isomers with C-2 upsilon symmetry, the other two are Linear chains with C-infinity upsilon symmetry. Meanwhile, two spin states for each isomer, that is, singlet and triplet for LaC3+, doublet and quartet for LaC3 and LaC32+, respectively, are also considered. Geometries, vibrational frequencies, infrared intensities, and other quantities are reported and discussed. The results indicate that at some spin states; the C-2 upsilon symmetry isomers are the dominant structures, while for the other spin states, linear isomers are energetically favored. (C) 1998 John Wiley & Sons, Inc.

Strongly nucleophilic RhI centre in square-planar complexes with terdentate (κ3) 2,2′:6′,2′′-terpyridine ligands: crystallographic, electrochemical and density functional theoretical studies

Rh-I-terpyridine complexes have been unambiguously formed for the first time. The 2,21:6',2"-terpyridine (tpy), 4'-chloro-2,2':6',2"-terpyridine (4'-Cl-tpy) and 4'-(tert-butyldimethylsilyl-ortho-carboranyl)-2,2':6',2"-terpyridine (carboranyl-tpy) ligands were used for successful syntheses and characterisation of the corresponding Rh-I complexes with halide coligands, [Rh(X)(4'-Y-terpyridine)] (X = Cl, Y = H, Cl, carboranyl; X = Br, Y = H). All four neutral Rh-tpy complexes are square planar, with Rh-X bonds in the plane of the 4'-Y-terpyridine ligands. Full characterisation of these dark blue, highly air-sensitive compounds was hampered by their poor solubility in various organic solvents. This is mainly due to the formation of pi-stacked aggregates, as evidenced by the crystal structure of [Rh(Cl)(tpy)]; in addition, [Rh(Cl)(carboranyl-tpy)] merely forms discrete dimers. The (bonding) properties of the novel Rh-I-terpyridine complexes have been studied with single-crystal X-ray diffraction, (time-dependent) density functional theoretical (DFT) calculations, far-infrared spectroscopy, electronic absorption spectroscopy and cyclic voltammetry. From DFT calculations, the HOMO of the studied Rh-I-terpyridine complexes involves predominantly the metal centre, while the LUMO resides on the terpyridine ligand. Absorption bands of the studied complexes in the visible region (400-900 nm) can be assigned to MLCT and MLCT/XLCT transitions. The relatively low oxidation potentials of [Rh(X)(tpy)] (X = Cl, Br) point to a high electron density on the metal centre. This makes the Rh-I-terpyridine complexes strongly nucleophilic and (potentially) highly reactive towards various (small) substrate molecules containing carbon-halide bonds.

Theoretical investigation of electronic and optical properties of andalusite within density functional theory

The electronic and optical properties of andalusite were studied by using quantum-mechanical calculations based on the density functional theory (DFT). The electronic structure shows that andalusite has a direct band gap of 5.01 eV. The complex dielectric function and optical constants, such as extinction coefficient, refractive index, reflectivity and energy-loss spectrum, are calculated. The optical properties of andalusite are discussed based on the band structure calculations. It is shown that the O-2p states and Al-3s states play a major role in optical transitions as initial and final states, respectively. (C) 2010 Elsevier Ltd. All rights reserved.

Testing phenomenological and theoretical models of dark matter density profiles with galaxy clusters

We use the stacked gravitational lensingmass profile of four high-mass (M 1015M ) galaxy clusters around z≈0.3 from Umetsu et al. to fit density profiles of phenomenological [Navarro– Frenk–White (NFW), Einasto, S´ersic, Stadel, Baltz–Marshall–Oguri (BMO) and Hernquist] and theoretical (non-singular Isothermal Sphere, DARKexp and Kang & He) models of the dark matter distribution. We account for large-scale structure effects, including a two-halo term in the analysis.We find that the BMO model provides the best fit to the data as measured by the reduced χ2. It is followed by the Stadel profile, the generalized NFW profile with a free inner slope and by the Einasto profile. The NFW model provides the best fit if we neglect the two-halo term, in agreement with results from Umetsu et al. Among the theoretical profiles, the DARKexp model with a single form parameter has the best performance, very close to that of the BMO profile. This may indicate a connection between this theoretical model and the phenomenology of dark matter haloes, shedding light on the dynamical basis of empirical profiles which emerge from numerical simulations.