Why [6,6]- and 1,2-Benzal-3-N-4-O-Cyclic Phenylimidate C-60 Undergo Electrochemically Induced Retro-Addition Reactions while 1,4-Dibenzyl-2,3-Cyclic Phenylimidate C-60 Does Not? C-H center dot center dot center dot X (X = N, O) Intramolecular Interactions in Organofullerenes

The electrochemical properties of a series of structurally related fullerooxazoles, [6,6] cyclic phenylimidate C-60 (1), 1,2-benzal-3-N-4-O-cyclic phenylimidate C-60 (2), and 1,4-dibenzyl-2,3-cyclic phenylimidate C-60 (3), are described, and the spectroscopic characterizations of their anionic species are reported. The results show that compounds I and 2 undergo retro-cycloaddition reactions that lead to the formation of C-60 and C61HPh, respectively, upon two-electron-transfer reduction. However, compound 3 demonstrates much more electrochemical stability as no retro-cycloaddition reaction occurs under similar conditions. Natural bond orbital (NBO) calculations on charge distribution show there is no significant difference among the dianions of 1, 2, and 3, indicating that the electrochemical stability of 3 is unlikely to be caused by the charge distribution difference of the dianions of three compounds. Examination on the crystal structure of compound 3 reveals close contacts of the C-H group with the heteroatoms (N and O) of cyclic phenylimidate, suggesting the existence of C-H center dot center dot center dot X (X = N, O) intramolecular hydrogen bonding among the addends, which is further confirmed by NBO analysis.

Electronic structures and chemical bonding in 4d transition metal monohalides

Bond distances, vibrational frequencies, dipole moments, dissociation energies, electron affinities, and ionization potentials of NIX (XM = Y-Cd, X = F, Cl, Br, I) molecules in neutral, positively, and negatively charged ions were studied by density functional method, B3LYP. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides ionic component, covalent bonds are formed between the 4d transition metal s, d orbitals, and the p orbital of halogen. For both neutral and charged molecules, the fluorides have the shortest bond distance, iodides the longest. Although the opposite situation is observed for vibrational frequency, that is, fluorides have the largest value, iodides the smallest. For neutral and anionic species, the dissociation energy tends to decrease with the increasing atomic number from Y to Cd, suggesting the decreasing or weakening of the bond strength. For cationic species, the trend is observed from Y to Ag.

Structure and identity of 4,4 '-thiobisbenzenethiol self-assembled monolayers

Self-assembled monolayers (SAMs) of 4,4'-thiobisbenzenethiol (TBBT) can be formed on Au surface spontaneously. The structural characteristics and adsorption behavior of TBBT SAMs on Au have been investigated by surface enhanced Raman scattering (SERS), electrochemical cyclic voltammetry (CV), ac impedance spectroscopy (EIS), and atomic force microscopy (AFM). It is demonstrated that TBBT adsorbed on Au by losing a H atom, forming one Au-S bond, and the other mercapto group is free at the surface of the monolayer owing to the presence of the nu(S-H) at 2513 cm(-1) and the delta(C-S-H) at 910 cm(-1) in SERS. The enhancement of the vibration of C-S (1064 cm(-1)), the aromatic C-H vibration (3044 cm(-1)), and the absence of the vibration of S-S illustrate TBBT adsorbed on Au forming a monolayer with one benzene ring tilted with respect to the Au surface. The interpretation of the observed frequencies is aided by ab initio molecular orbital (MO) calculations at the HF/6-31G* level of theory. Electrochemical CV and EIS indicate TBBT monolayers can passivate the Au effectively for its low ratio of pinhole defects (theta = 99.6%). AFM studies give details about the surface morphology. The applications of TBBT SAMs have been extensively investigated by exposure of Cu2+ ion to TBBT SAMs on Au and covalent adsorption of metal nanoparticles.

Local similarity in organic crystals and the non-uniqueness of X-ray powder patterns

Two new concepts for molecular solids, 'local similarity' and 'boundary-preserving isometry', are defined mathematically and a theorem which relates these concepts is formulated. 'Locally similar' solids possess an identical short-range structure and a 'boundary-preserving isometry' is a new mathematical operation on a finite region of a solid that transforms mathematically a given solid to a locally similar one. It is shown further that the existence of such a 'boundary-preserving isometry' in a given solid has infinitely many 'locally similar' solids as a consequence. Chemical implications, referring to the similarity of X-ray powder patterns and patent registration, are discussed as well. These theoretical concepts, which are first introduced in a schematic manner, are proved to exist in nature by the elucidation of the crystal structure of some diketopyrrolopyrrole (DPP) derivatives with surprisingly similar powder patterns. Although the available powder patterns were not indexable, the underlying crystals could be elucidated by using the new technique of ab initio prediction of possible polymorphs and a subsequent Rietveld refinement. Further ab initio packing calculations on other molecules reveal that 'local crystal similarity' is not restricted to DPP derivatives and should also be exhibited by other molecules such as quinacridones. The 'boundary-preserving isometry' is presented as a predictive tool for crystal engineering purposes and attempts to detect it in crystals of the Cambridge Structural Database (CSD) are reported.

Theoretical investigation on the adsorption of Ag+ and hydrated Ag+ cations on clean Si(111) surface

In this paper, the adsorption of Ag+ and hydrated Ag+ cations on clean Si(111) surface were investigated by using cluster (Gaussian 03) and periodic (DMol(3)) ab initio calculations. Si(111) surface was described with cluster models (Si14H17 and Si22H21) and a four-silicon layer slab with periodic boundary conditions. The effect of basis set superposition error (BSSE) was taken into account by applying the counterpoise correction. The calculated results indicated that the binding energies between hydrated Ag+ cations and clean Si(111) surface are large, suggesting a strong interaction between hydrated Ag+ cations and the semiconductor surface. With the increase of number, water molecules form hydrogen bond network with one another and only one water molecule binds directly to the Ag+ cation. The Ag+ cation in aqueous solution will safely attach to the clean Si(111) surface.

Addition reactions of nitrones on the reconstructed C(100)-2 x 1 surfaces

In this paper, the reactions of nitrone, N-methyl nitrone, N-phenyl nitrone and their hydroxylamine tautomers (vinyl-hydroxylamine, N-methyl-vinyl-hydroxylamine and N-phenyl-vinyl-hydroxylamine) on the reconstructed C(100)-2 x 1 surface have been investigated using hybrid density functional theory (B3LYP), Moller-Plesset second-order perturbation (MP2) and multi-configuration complete-active-space self-consistent-field (CASSCF) methods. The calculations showed that all the nitrones can react with the surface "dimer" via facile 1.3-dipolar cycloaddition with small activation barriers (less than 12.0 kJ/mol at B3LYP/6-31g(d) level). The [2+2] cycloaddition of hydroxylamine tautomers on the C(100) surface follows a diradical mechanism. Hydroxylamine tautomers first form diradical intermediates with the reconstructed C(I 00)-2 x I surface by overcoming a large activation barrier of 50-60 kJ/mol (B3LYP), then generate [2+2] cycloaddition products via diradical transition states with negligible activation barriers. The surface reactions result in hydroxyl or amino-terminated diamond surfaces, which offers new opportunity for further modifications. (C) 2007 Elsevier B.V. All rights reserved.

Photodissociation of bromobenzene at 266 nm

The photodissociation of C6H5Br at 266 nm has been investigated on the universal crossed molecular beam machine, and time-of-flight spectra as well as the angular distribution of Br atom have been measured. Photofragment translational energy distribution P(E-t) reveals that about 47% of the available energy is partitioned into translational energy. The anisotropy parameter beta at this wavelength is -0.7+/-0.2. From P(E-t) and beta, we deduce that C6H5Br photodissociation is a fast process and the transition dipole moment is almost perpendicular to the C-Br bond. Ab initio calculations have been performed, and the calculated results show that the geometry of the first excited state of bromobenzene has changed apparently compared with that of the ground state. Two kinds of possible fast dissociation mechanism have also been proposed. (C) 1999 American Institute of Physics. [S0021-9606(99)01206-4].

Columnar-to-disk structural transition in nanoscale (SiO2)(N) clusters

Bromley, S. T., Flikkema, E. (2005) 'Columnar-to-disk structural transition in nanoscale (SiO2)(N) clusters'. Physical Review Letters 95 (18), article no: 185505 RAE2008

Computational modeling of defects in nanoscale device materials

This PhD thesis concerns the computational modeling of the electronic and atomic structure of point defects in technologically relevant materials. Identifying the atomistic origin of defects observed in the electrical characteristics of electronic devices has been a long-term goal of first-principles methods. First principles simulations are performed in this thesis, consisting of density functional theory (DFT) supplemented with many body perturbation theory (MBPT) methods, of native defects in bulk and slab models of In0.53Ga0.47As. The latter consist of (100) - oriented surfaces passivated with A12O3. Our results indicate that the experimentally extracted midgap interface state density (Dit) peaks are not the result of defects directly at the semiconductor/oxide interface, but originate from defects in a more bulk-like chemical environment. This conclusion is reached by considering the energy of charge transition levels for defects at the interface as a function of distance from the oxide. Our work provides insight into the types of defects responsible for the observed departure from ideal electrical behaviour in III-V metal-oxidesemiconductor (MOS) capacitors. In addition, the formation energetics and electron scattering properties of point defects in carbon nanotubes (CNTs) are studied using DFT in conjunction with Green’s function based techniques. The latter are applied to evaluate the low-temperature, low-bias Landauer conductance spectrum from which mesoscopic transport properties such as the elastic mean free path and localization length of technologically relevant CNT sizes can be estimated from computationally tractable CNT models. Our calculations show that at CNT diameters pertinent to interconnect applications, the 555777 divacancy defect results in increased scattering and hence higher electrical resistance for electron transport near the Fermi level.

Uncovering compounds by synergy of cluster expansion and high-throughput methods.

Predicting from first-principles calculations whether mixed metallic elements phase-separate or form ordered structures is a major challenge of current materials research. It can be partially addressed in cases where experiments suggest the underlying lattice is conserved, using cluster expansion (CE) and a variety of exhaustive evaluation or genetic search algorithms. Evolutionary algorithms have been recently introduced to search for stable off-lattice structures at fixed mixture compositions. The general off-lattice problem is still unsolved. We present an integrated approach of CE and high-throughput ab initio calculations (HT) applicable to the full range of compositions in binary systems where the constituent elements or the intermediate ordered structures have different lattice types. The HT method replaces the search algorithms by direct calculation of a moderate number of naturally occurring prototypes representing all crystal systems and guides CE calculations of derivative structures. This synergy achieves the precision of the CE and the guiding strengths of the HT. Its application to poorly characterized binary Hf systems, believed to be phase-separating, defines three classes of alloys where CE and HT complement each other to uncover new ordered structures.

12C2H2-Ar van der Waals complex

New theoretical and experimental results on the acetylene-Ar van der Waals complex are presented and the literature is reviewed. New ab initio calculations at the MP2 level were performed using large basis sets with diffuse functions and taking into account the basis set superposition error. It was found that the structure of acetylene is not significantly altered by the complexation and that its vibrational frequencies are only slightly lowered. Finally, it was observed that the calculated properties of the complex (structure, vibrational spectrum, bond dissociation energy) are not sensitive to the structure imposed on acetylene. Experimentally, acetylene-Ar was produced in a supersonic expansion under experimental conditions corresponding to 9 K rotational temperature. Thanks to the performances of CW-CRDS detection, the Ka = 0 ← 1, 1 ← 0, and 2 ← 1 sub- bands of the v1 + v3 band could be recorded and resolved and most of their lines assigned. Upper-state rotational constants were fitted, however not including the upper Ka = 2 state, which shows K-doubling the opposite of the expected. The Lorentzian width of most line profiles sets the mean lifetime to some 7.5 ns. Local perturbations affecting line positions and/or line widths are demonstrated. Additional series of lines tentatively attributed to acetylene-Ar are discussed.© 2009 American Chemical Society.

Accurate ground-state potential energy surfaces of the C2H2–Kr and C2H2–Xe van der Waals complexes

Accurate ab initio intermolecular potential energy surfaces (IPES) have been obtained for the first time for the ground electronic state of the C 2H2-Kr and C2H2-Xe van der Waals complexes. Extensive tests, including complete basis set and all-electron scalar relativistic results, support their calculation at the CCSD(T) level of theory, using small-core relativistic pseudopotentials for the rare-gas atoms and aug-cc-pVQZ basis sets extended with a set of 3s3p2d1f1g mid-bond functions. All results are corrected for the basis set superposition error. The importance of the scalar relativistic and rare-gas outer-core (n.1)d correlation effects is investigated. The calculated IPES, adjusted to analytical functions, are characterized by global minima corresponding to skew T-shaped geometries, in which the Jacobi vector positioning the rare-gas atom with respect to the center of mass of the C2H2 moiety corresponds to distances of 4.064 and 4.229Å, and angles of 65.22° and 68.67° for C 2H2-Kr and C2H2-Xe, respectively. The interaction energy of both complexes is estimated to be -151.88 (1.817 kJ mol-1) and -182.76 cm-1 (2.186 kJ mol-1), respectively. The evolution of the topology of the IPES as a function of the rare-gas atom, from He to Xe, is also discussed. © 2012 Taylor and Francis.

Multiple proton translocation in biomolecular systems: concerted to stepwise transition in a simple model

In this paper we study a simple model potential energy surface (PES) useful for describing multiple proton translocation mechanisms. The approach presented is relevant to the study of more complex biomolecular systems like enzymes. In this model, at low temperatures, proton tunnelling favours a concerted proton transport mechanism, while at higher temperatures there is a crossover from concerted to stepwise mechanisms; the crossover temperature depends on the energetic features of the PES. We illustrate these ideas by calculating the crossover temperature using energies taken from ab initio calculations on specific systems. Interestingly, typical crossover temperatures lie around room temperature; thus both concerted and stepwise reaction mechanisms should play an important role in biological systems, and one can be easily turned into another by external means such as modifying the temperature or the pH, thus establishing a general mechanism for modulation of the biomolecular function by external effectors.

R-matrix theory of electron molecule scattering

This paper presents an overview of R-matrix theory of electron scattering by diatomic and polyatomic molecules. The paper commences with a detailed discussion of the fixed-nuclei approximation which in recent years has been used as the basis of the most accurate ab initio calculations. This discussion includes an overview of the computer codes which enable electron collisions with both diatomic and polyatomic molecules to be calculated. Nuclear motion including rotational and vibrational excitation and dissociation is then discussed. In non-resonant energy regions, or when the scattered electron energy is not close to thresholds, the adiabatic-nuclei approximation can be successfully used. However, when these conditions are not applicable, non-adiabatic R-matrix theory must be used and a detailed discussion of this theory is given. Finally, recent applications of the theory to treat electron scattering by polyatomic molecules are reviewed and a detailed comparison of R-matrix calculations and experimental measurements for water is presented.

Multiple Evidence for Gold(I)center dot center dot center dot Silver(I) Interactions in Solution

[AuAg3(C6F5)(CF3CO2)(3)(CH2PPh3)](n) (2) was prepared by reaction of [Au(C6F5)(CH2PPh3)] (1) and [Ag(CF3CO2)] (1:3). The crystal structures of complexes I and 2 were determined by X-ray diffraction, and the latter shows a polymeric 2D arrangement built by Au - Ag, Ag - Ag, and Ag - O contacts. The metallophilic interactions observed in 2 in the solid state seem to be preserved in concentrated THF solutions, as suggested by EXAFS, pulsed-gradient spin-echo NMR, and photophysical studies, which showed that the structural motif [AuAg3(C6F5)(CF3CO2)(3)(CH2PPh3)] is maintained under such conditions. Time-dependent DFT calculations agree with the experimental photophysical energies and suggest a metal-to-ligand charge-transfer phosphorescence process. Ab initio calculations give an estimated interaction energy of around 60 kJ mol(-1) for each Au - Ag interaction.