Prospects for resolving chemical structure by atomic force microscopy: a first-principles study

In a recent paper, the chemical structure of a molecule was resolved by means of atomic force microscopy (AFM): using a metal tip terminated in a CO molecule, the authors could image the internal bonding arrangement of a pentacene molecule with remarkable spatial resolution (notably better than with other tip terminations), as verified by their first-principles calculations. Here we further explore with first-principles calculations the mechanisms, applicability, and capabilities of this approach for a wider range of situations, by varying the imaged molecule and the tip beyond the experimental cases. In our simulations, a high atomic resolution is found to be dominated by the electronic structure of the last two atoms on the tip apex which are set perpendicularly to the sample molecule. For example, tips terminated in CH(4) or pentacene itself (both having a C-H apex) yield similar images, while tips terminated in O(2) or CO give quite different images. While using a CO-terminated tip successfully resolves the chemical structure of pentacene and of other extended planar networks based on C(6) rings, this tip fails to resolve the structures of benzene (with its single C(6) ring) or nonplanar C(6) networks, such as C(60) or small-diameter carbon nanotubes. Defects (such as N substitution for a C-H group) were also found to significantly influence the image resolution. Our findings indicate that further application of this approach requires, for each sample, careful selection of a suitable "imaging" molecule as tip termination.     

SiC-doped boron nitride nanotubes: computations of 11B and 14N quadrupole coupling constants

Abstract  

Density-functional theory calculations have been performed to investigate the properties of the electronic structures of silicon–carbon-doped boron nitride nanotubes (BNNTs). The geometries of zigzag and armchair BNNTs were initially optimized and the quadrupole coupling constants subsequently calculated. The results indicate that doping of B and N atoms by C and Si atoms has more influence on the electronic structure of the BNNTs than does doping of B and N atoms by Si and C atoms. The changes of the electronic sites of the N atoms are also more significant than those of the B atoms.     

Computational studies of effects of tubular lengths on the NMR properties of pristine and carbon decorated boron phosphide nanotubes

Density functional theory (DFT) calculations were performed to investigate the effects of tubular lengths on the nuclear magnetic resonance (NMR) properties of boron phosphide (BP) nanotubes. To this aim, the properties of pristine and carbon decorated (C-decorated) models of representative zigzag and armchair BP nanotubes were investigated. The results indicated that the atoms at the edges of nanotubes do not detect any significant changes. The NMR properties of boron atoms only detect slight changes but those of phosphorous atoms are more notable.     

Disiline-doped boron nitride nanotubes: A computational study

The properties of the electronic structure of the Disiline-doped boron nitride nanotubes (Disiline-BNNTs) are investigated by a density functional theory (DFT) calculation. The structural forms are firstly optimized and the CS tensors calculated. Subsequently, the chemical-shielding isotropic (CS^I) and chemical shielding anisotropic (CS^A) parameters are found. The shielding values of boron (B) and nitrogen (N) atoms were calculated by Gauge-Including Atomic Orbital (GIAO), Continuous Set of Gauge Transformations (CSGT) and Individual Gauges for Atoms in Molecules (IGAIM) methods, using B3LYP/6-311+G*. The B3LYP level of theory with IGAIM was the best method to evaluate the theoretical chemical shifts for studied models. The results reveal a significant effect of Disiline doping on the chemical shielding tensors at the sites of those ¹¹B and ¹⁵N nuclei located in the nearest neighborhood of the Disiline-doped ring. Furthermore, the values of dipole moments and HOMO-LUMO gaps change in the Disiline-doped models in comparison with the original pristine model.     

Stabilities in field electron emissions from noble‐metal covered W nano‐tips: apex structure dependence

We observed field emission microscopy (FEM) patterns of noble‐metal (NM) covered W nano‐tips with three different apex structures fabricated by field evaporation. Each of the three tips was terminated with a single atom, three atoms or ten atoms. We investigated the temporal changes in the FEM of these tips to discuss the stabilities in the spatial distributions of the field emission (FE) beams. The single‐atom tip showed two characteristics that were superior to the others. First, the beams emitted from the single‐atom tip were the most collimated among the three tips (the semi‐cone angle of 1.0° , FWHM). Second, adsorption of residual gas had little influence on FE from the single‐atom tip, while the other tips were easily contaminated even at ultra high vacuum, resulting in the emission fluctuation. Copyright © 2006 John Wiley & Sons, Ltd.     

Molecular structures of arachno-heteroboranes with decaborane frameworks: two Cs-symmetrical azacarba- and carbathiaboranes

The gas-phase structure of 6,9-CSB8H12 has been determined by electron diffraction and ab initio calculations, and that of 6,9-CNB8H13 has also been calculated. The accuracy of each structure has been confirmed by 11B NMR calculations. The position of the sulfur atom is very close to that of the boron atom occupying the equivalent position in the parent molecule [B10H14](2-), reflecting the similarity of sizes of sulfur and boron atoms. The nitrogen and carbon atoms, on the other hand, lie much closer to the centers of the cages. The B8-X9-B10 angles increase from 98.7 degrees for X = S to 122.8 degrees for X = N. There are also large changes in relative lengths of bonds, with some bonds lengthening by up to 14.6 pm on introduction of a sulfur atom.     

NMR parameters of SiC-doped (6,0) zigzag single-walled boron phosphide nanotubes: a density functional study

Abstract  

Nuclear magnetic resonance (NMR) parameters including isotropic and anisotropic chemical shielding parameters and electronic structures were calculated using density functional theory (DFT) for silicon–carbide-doped boron phosphide nanotubes. Geometry optimizations were carried out at the B3LYP/6-31G* level of theory using the Gaussian 03 program suite. The isotropic and anisotropic chemical shielding parameters were calculated for the sites of various ¹³C, ²⁹Si, ¹¹B, and also ³¹P atoms in pristine and SiC-doped (6,0) zigzag boron phosphide nanotube models. The calculations indicated that doping of ¹¹B and ³¹P atoms by C and Si atoms had a more significant influence on the calculated shielding tensors than did doping of the B and P atoms by Si and C atoms. In comparison with the pristine model, Si- and C-doping of P and B sites of the zigzag nanotubes reduces the energy gaps of the nanotubes and increases their electrical conductance.     

A computational study of aluminum phosphide nanotubes

Electronic structures of two representative zigzag and armchair models of aluminum phosphide nanotube (AlPNT) were investigated by density functional theory calculations. The structures were optimized and the bond lengths, tip diameters, band gaps, and dipole moments were calculated. Moreover, the quadrupole coupling constants (C_Q) were calculated for the Al‐27 atoms of the optimized structures. The same values of Al? P bond lengths were calculated for both models. The larger value of band gap of armchair model than the zigzag model indicated the stronger dielectric property for the former model. The values of C_Q(²⁷Al) were the largest for the Al atoms placed at the tips of both zigzag and armchair AlPNT than other Al atoms, which could reveal dominant role of the Al atoms placed at the tips of nanotube in determining the electronic properties of the AlPNT. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Probing lead(II) bonding environments in 4-substituted pyridine adducts of (2,6-Me2C6H3S)2Pb: an X-ray structural and solid-state 207Pb NMR study

The effect of subtle changes in the sigma-electron donor ability of 4-substituted pyridine ligands on the lead(II) coordination environment of (2,6-Me(2)C(6)H(3)S)(2)Pb (1) adducts has been examined. The reaction of 1 with a series of 4-substituted pyridines in toluene or dichloromethane results in the formation of 1:1 complexes [(2,6-Me(2)C(6)H(3)S)(2)Pb(pyCOH)](2) (3), [(2,6-Me(2)C(6)H(3)S)(2)Pb(pyOMe)](2) (4), and (2,6-Me(2)C(6)H(3)S)(2)Pb(pyNMe(2)) (5) (pyCOH = 4-pyridinecarboxaldehyde; pyOMe = 4-methoxypyridine; pyNMe2 = 4-dimethylaminopyridine), all of which have been structurally characterized by X-ray crystallography. The structures of 3 and 4 are dimeric and have psi-trigonal bipyramidal S(3)N bonding environments, with the 4-substituted pyridine nitrogen and bridging sulfur atoms in axial positions and two thiolate sulfur atoms in equatorial sites. Conversely, compound 5 is monomeric and exhibits a psi-trigonal pyramidal S(2)N bonding environment at lead(II). The observed structures may be rationalized in terms of a simple valence bond model and the sigma-electron donor ability of the 4-pyridine ligands as derived from the analysis of proton affinity values. Solid-state (207)Pb NMR experiments are applied in combination with density functional theory (DFT) calculations to provide further insight into the nature of bonding in 4, 5, and (2,6-Me(2)C(6)H(3)S)(2)Pb(py)(2) (2). The lead chemical shielding (CS) tensor parameters of 2, 4, and 5 reveal some of the largest chemical shielding anisotropies (CSA) observed in lead coordination complexes to date. DFT calculations using the Amsterdam Density Functional (ADF) program, which take into account relativistic effects using the zeroth-order regular approximation (ZORA), yield lead CS tensor components and orientations. Paramagnetic contributions to the lead CS tensor from individual pairs of occupied and virtual molecular orbitals (MOs) are examined to gain insight into the origin of the large CSA. The CS tensor is primarily influenced by mixing of the occupied MOs localized on the sulfur and lead atoms with virtual MOs largely comprised of lead 6p orbitals.     

BN-Substituted fullerenes C60−2x (BN) x : a computational 11B and 15N NMR study

Density functional theory has been used to investigate the ¹⁵N and ¹¹B NMR parameters of heterofullerenes C_60?2x (BN) _x (x = 1, 2, 3, 6, 9, 12, 15, 18, 21, and 24). Geometry structures of all the BN-substituted fullerenes have been optimized at the B3LYP/6-31+G* level of theory. Afterward, ¹¹B and ¹⁵N chemical shielding isotropy and anisotropy (CSI, CSA) parameters have been calculated at the same level. The obtained results illustrate the electrostatic environment divisions of the nuclei into few layers, which have been then confirmed by calculating natural charges at B and N sites. A good correlation has been seen between the layers of CSI and CSA values and three local structures around boron and nitrogen atoms. The effects of curvature of fullerene structure on chemical shielding (CS) parameters of heterofullerenes have also been investigated by computing CS tensors for curved and relaxed structures of a set of small fragments separated from the heterofullerenes, suggesting high sensitivity of CS parameters to the curvature of fullerene structure.     

DFT calculations of NMR properties for GaP nanotubes

Abstract  

We performed density functional theory calculations for nitrogen-doped models of the representative structures of (6,0) zigzag and (4,4) armchair aluminum phosphide nanotubes (AlPNTs). Our results indicate that the optimized bond distances and tip diameters do not detect the effects of the N-doped regions; however, the effects are observed for the band gap energies and dipole moments. It is noted that substitution of the P atom by the N atom does not influence the value of band gap energy for this N-doped model. The results also indicate that the tendency of the Al atom for contribution to the Al–N bond is stronger than the tendency of the P atom for contribution to the N–P bond; therefore, the latter form of substitution makes the AlPNTs interesting as reactive materials towards other atoms or molecules, especially for the the zigzag AlPNT.     

A solid-state nitrogen-15 NMR and ab initio study of nitrobenzenes

Insight into the unexpectedly small range of isotropic nitrogen chemical shifts in nitrobenzene derivatives is gained through measurements of the chemical shift (CS) tensor by solid-state NMR experiments and ab initio molecular orbital (MO) and density functional theory (DFT) calculations. The principal components, delta(ii), of the (15)N CS tensors have been measured for nitrobenzene, 4-nitroaniline, 4-nitrotoluene, 4-nitroanisole, 4-nitroacetophenone, nitromesitylene, and 2,4,6-tri-tert-butylnitrobenzene. No obvious correlations of the delta(ii) values with traditional reactivity parameters were observed. The CS tensor components change significantly for the para-substituted nitrobenzenes, but these variations nearly cancel to yield isotropic shifts that fall in a range of only 3 ppm. Ab initio calculations of the delta(ii) values at the HF level are in poor agreement with the experimental values, whereas MP2 calculations and DFT calculations employing the B3LYP functional are in better agreement with experiment. The calculated (B3LYP/6-311G) delta(ii) values follow a trend in which delta(11) and delta(33) increase while delta(22) decreases with the accepted electron withdrawing ability of the para substituent. These changes tend to cancel yielding a variation in delta(iso) of only 4 ppm. These calculations indicate that the CS tensor has the same orientation as the carbon CS tensor in the isoelectronic benzoate anion: delta(11) bisects the O-N-O angle, delta(33) is perpendicular to the NO(2) plane, and delta(22) is in the NO(2) plane and perpendicular to delta(11).     

Influence of Mn-doping on the chemical shielding tensors of Ga and N in the armchair GaN nanotubes: A DFT study

The chemical shielding (CS) tensors of Gallium-71 and nitrogen-15 are computed for the first time in order to investigate the influence of Mn-doping on the electronic properties of the (5, 5) Gallium nitride nanotube (GaNNT). A GaNNT consisting of 40 Ga and 40 N atoms and having a 1.2 nm length was considered. One portal of the nanotube was capped by ten hydrogen atoms and other-end was kept open. Additionally, two other forms of this model of Mn-doped GaNNT were considered where a Mn-atom was substituted for a Ga atom either in the first or in the second layer. The calculations reveal that in both models of Mn-doped GaNNTs, the N atoms that are directly connected to the Mn atom have the smallest isotropic chemical shielding among other N atoms. These calculations were performed at the level of the density functional theory (DFT) using GAUSSIAN 03 package. The basis sets for Ga and N atoms were chosen to be 6-31G (d) and those for Mn atom were chosen to be LanL2DZ.     

Studies on the encapsulation of F- in single walled nanotubes of different chiralities using density functional theory calculations and Car-Parrinello molecular dynamics simulations

In this study, the encapsulation of F(-) in different nanotubes (NTs) has been investigated using electronic structure calculations and Car-Parrinello molecular dynamics simulations. The carbon atoms in the single walled carbon nanotube (CNT) are systematically doped with B and N atoms. The effect of the encapsulation of F(-) in the boron nitride nanotube (BNNT) has also been investigated. Electronic structure calculations show that the (7,0) chirality nanotube forms a more stable endohedral complex (with F(-)) than the other nanotubes. Evidence obtained from the band structure of CNT calculations reveals that the band gap of the CNT is marginally affected by the encapsulation. However, the same encapsulation significantly changes the band gap of the BNNT. The density of states (DOS) derived from the calculations shows significant changes near the Fermi level. The snapshots obtained from the CPMD simulation highlight the fluctuation of the anion inside the tube and there is more fluctuation in BNNT than in CNT.     

A computational investigation of 11B electric field gradient and chemical shielding tensors as well as NBO analysis in the B80 fullerene

Using first-principles calculations within the frame of the density functional theory, we analyze electronic properties of the boron fullerene B80, based on NMR, NQR parameters and NBO analysis. Our results show three typical ranges for boron chemical shielding parameters corresponding to each of the nonequivalent magnetic sites of the B atoms. These three sites are related to frame atoms and two sets of atoms capping hexagons, endohadral and exohedral caps. Calculating quadrupole coupling components confirm this conclusion with more sensitivity than chemical shielding parameters. In addition calculated asymmetry parameter shows that EFG tensor for boron atoms capping hexagons is axially symmetric, η ≈ 0, while this tensor becomes considerably asymmetric for frame atoms, η = 0.95, as a result of charge transfer from 20 boron atoms capping hexagons to the 60 frame atoms.     

Reactions of B atoms and clusters with NO: experimental and theoretical characterization of novel molecules containing B, N, and O

Reactions of boron atoms and clusters with NO molecules in solid argon have been studied using matrix isolation infrared absorption spectroscopy. The reaction products were identified by isotopic substitution ((10)B, (11)B, (15)N(16)O, (14)N(18)O, and mixtures) and comparison with density functional calculations of isotopic frequencies. In solid argon, boron atoms spontaneously reacted with NO to form the insertion molecule NBO. The BNBO and OBNNO molecules were formed by the B and NO addition reactions to NBO. The linear BBNO and BBBNO nitrosyls also were formed spontaneously on annealing. These molecules photochemically rearranged to the more stable BNBO and BNBBO isomers, which have linear polyyne-like structures. The photosensitive OBNNO molecule decomposed to form the NNBO(2) van der Waals complex. In addition, the novel OBON diradical was also formed on photolysis in high-concentration NO experiments.     

Computational NQR study of a boron nitride nanocone

Abstract  

The electronic structure of a boron nitride nanocone with 240° disclination, and some properties that derive from this structure, were studied by density-functional theory calculations. In the considered model there are only hexagonal rings, with the apex and mouth of the nanocone saturated by hydrogen atoms. The model was optimized, and then the nuclear quadrupole resonance parameters were calculated at the sites of ¹¹B and ¹⁴N nuclei. The results revealed that the nuclei in the boron nitride nanocone are divided into layers with similar electronic properties. The nuclei at the apex and mouth are very important for the electronic behavior of the nanocone, with ¹¹B playing the major role.     

Theoretical study on the mechanism of the gas-phase reaction of diborane(3) anion with carbon disulfide

The complex potential energy surface of the gas-phase reaction of HB(H)BH- with CS2 to give three low-lying products [B2H3S]- + CS, [BH2CS]- + HBS, and [BH3CS] + BS-, involving nine [B2H3CS2]- isomers and 12 transition states, has been investigated at the CCSD(T)/6-311++G(d,p)/B3LYP/6-311++G(d,p) level. Our calculations are in harmony with the recent experimental and theoretical results, and reveal some new bonding and kinetic features of this reaction system. Our theoretical results may help the further identification of the products [BH2CS]- + HBS and [BH3CS] + BS- and may provide useful information on the chemical behaviors of other electron-deficient boron hydride anions.     

Adsorption of the nitrosamine and thionitrosamine molecules as carcinogen compounds on the BN and B3Al N nanotubes: A DFT study

DFT calculations were performed to investigation of the influence of doping three atoms of aluminum on the electronic properties of the (4,0) zigzag boron nitride nanotube (BNNT). Also, adsorption properties of nitrosamine (NA) and thionitrosamine (TNA) molecules as carcinogen agents onto BN and B_Al3N nanotubes were studied. The results show that the B_3AlN nanotube is the most energetically favorable candidates for adsorption of these molecules. Also, B(B_3Al)NNT/TNA complexes are more stable than B(B_3Al)NNT/NA complexes. The HOMO–LUMO gap, electronic chemical potential (μ), hardness (?), softness (S), the maximum amount of electronic charge (ΔN_max) and electrophilicity index (ω) for monomers and complexes in the gas and polar solvent phases were calculated. The results show that the conductivity and reactivity of BNNT increase by doping Al atoms instead of B atoms. Also, the interaction of NA and TNA molecules with BN and B_Al3N nanotubes results in significant changes in the electronic properties of nanotubes. Based on the natural bond orbital (NBO) analysis, in all complexes charge transfer occurs from NA and TNA molecules to nanotubes. Theory of atoms in molecules (AIM) was applied to characterize the nature of interactions in nanotubes. It is predicted that, BN and B_3AlN nanotubes can be used to as sensor for detection of NA and TNA molecules.