Ab initio Hartree-Fock and density functional theory calculations were carried out to investigate the structures, energies, and vibrational spectra of indole and two of its hydrogen migration tautomers. The calculated results of indole are in good agreement with experiments. Rotational constants and infrared spectral features of 2H-indole and 3H-indole are predicted to assist future experimental identification of the two tautomers. Transition states of unimolecular isomerization among the three tautomers are also optimized and activation barriers of the isomerization reactions evaluated. The results indicate that unimolecular indole → 3H-indole proceeds via 2H-indole with an activation barrier of 51 kcal/mol.

The molecular structures and vibrational spectra of Dewar benzene, benzvalene, trimethylenecyclopropane, prismane and 3,4-dimethylenecyclobutene have been investigated by density functional theory using Becke's exchange with Lee-Yang-Parr's correlation functional and the 6-31G* basis set. Both the calculated structural parameters and vibrational frequencies are in good agreement with available experimental data. On the basis of the agreement between the calculated and experimental results, assignments of fundamental vibrational frequencies of Dewar benzene, benzvalene, and trimethylenecyclopropane were examined and some reassignments are proposed. The calculations also predict prominent IR and Raman spectral features of prismane and 3,4-dimethylenecyclobutene, which can assist experimental identification of these compounds and the assignment of observed spectral features when they are available.

Density functional theory (using Becke's exchange and Lee-Yang-Parr's correlation functionals (BLYP)) and ab initio Hartree-Fock calculations were carried out in order to investigate the molecular structure and vibrational spectra of 9,10-anthraquinone and its perdeuterated analog. The calculated structural and spectral features are in good agreement with the available experimental results. Most of the BLYP/6-31G* non-CH(D) stretching frequencies are slightly lower than reliable experimental assignments; the mean absolute deviation is about 14 cm-1. On the basis of agreement between calculated and experimental results, assignments of the fundamental vibrational modes were examined and some reassignments were proposed. The calculated results can serve as a guide for a future experimental search for the missing fundamentals of the target molecules.

Comparison of the observed and calculated vibrational frequencies of all-trans-octatetraene indicates that the density functional theory (DFT) using Becke's exchange and Lee-Yang-Parr's correlation functionals is as accurate as the Hartree-Fock (HF)-based scaled quantum mechanical force field approach in predicting fundamental vibrational frequencies. As the DFT calculation does not use any empirical parameters pertaining to the subject molecule and its computational cost scales more favorably than that of the HF theory, it is a more promising approach to molecular vibrational problems and should replace the empirical normal coordinate analysis for assisting vibrational assignments.

Small clusters of [6,6] phenyl-C61-butyric acid methyl ester (PCBM) molecules are analyzed with respect to their equilibrium geometries and associated electronic as well as energetic properties. Plane wave density functional theory (PWDFT) computations, assisted by molecular dynamics (MD) simulations, are performed on systems of the form PCBMn (n = 1-5). The bonding operative in these units is described as a cooperation between HO bonding, involving the C5H9O2 groups of the PCBM molecule, and fullerene-fullerene attraction. The maximally stable structures identified tend to include a dimer motif that combines both interaction modes. The great importance of van-der-Waals effects in stabilizing the studied clusters is demonstrated by comparing the PCBM3 series with and without inclusion of a van-der-Waals term in the PWDFT procedure. The two approaches yield reverse orders of stability. A decreasing tendency in the Kohn-Sham HOMO-LUMO gaps of PCBMn with the cluster size may be used to monitor PCBM aggregation in the active layer of organic photovoltaic devices by optical spectroscopy.

A combination of quantum chemical calculation and molecular dynamics simulation is applied to compute refractive indices of liquid-forming silicon oils. The densities of these species are obtained from molecular dynamics simulations based on the NPT ensemble while the molecular polarizabilities are evaluated by density functional theory. This procedure is shown to yield results well compatible with available experimental data, suggesting that it represents a robust and economic route for determining the refractive indices of liquid-forming organic complexes containing silicon.

The structures of endohedral complexes of the polyhedral oligomeric silsesquioxane (POSS) cage molecule (HSiO 3/2) 12, with both D 2d and D 6h starting cage symmetries, containing the atomic or ionic species: Li 0, Li +, Li -, Na 0, Na +, Na -, K 0, K +, K -, F -, Cl -, Br -, He, Ne, Ar were optimized by density functional theory using B3LYP and the 6-311G(d,p) and 6-311 ++G(2d,2p) basis sets. The exohedral Li +, Na +, K +, K -, F -, Cl -, Br -, He, Ne, Ar complexes, were also optimized. The properties of these complexes depend on the nature of the species encapsulated in, or bound to, the (HSiO 3/2) 12 cage. Noble gas (He, Ne and Ar) encapsulation in (HSiO 3/2) 12 has almost no effect on the cage geometry. Alkali metal cation encapsulation, in contrast, exhibits attractive interactions with cage oxygen atoms, leading to cage shrinkage. Halide ion encapsulation expands the cage. The endohedral X@(HSiO 3/2) 12 (X = Li +, Na +, K +, F -, Cl -, Br -, He and Ne) complexes form exothermically from the isolated species. The very low ionization potentials of endohedral Li 0, Na 0, K 0 complexes suggest that they behave like "superalkalis". Several endohedral complexes with small guests appear to be viable synthetic targets. The D 2d symmetry of the empty cage was the minimum energy structure in accord with experiment. An exohedral fluoride penetrates the D 6h cage to form the endohedral complex without a barrier.

Computational investigations on semiconductor (silicon or germanium) clusters (Sinor Gen) in combination with transition metal (M) impurities are reviewed in this contribution. Emphasis is placed on investigations that focus on the size evolution features of MmSi n(or MmGen) such as the critical ligand number for the transition from exohedral to endohedral equilibrium geometry. Geometric, energetic, electronic, and magnetic characteristics of MmSi n or MmGen systems are discussed. It is pointed out that selected MmSin systems with n = 12 and n = 16 and MmGen with n = 10 or 12 and n = 16 emerge from present computational research in the size region of n ≤ 20 as the most promising candidates for building blocks of novel nanomaterials. In addition, comparison is made between MmSin and MmGen clusters.

The lack of catalytic efficiency towards the complete ethanol oxidation reaction (EOR) has hindered the development of direct ethanol fuel cells (DEFCs). Ir-based catalysts have recently been shown promise in the complete EOR. However, the reaction mechanism of the complete EOR remains unclear, which impedes the development of better Ir-based catalysts. Herein, we performed extensive density functional theory (DFT) calculations to develop a comprehensive reaction network of EOR on Ir(100). The EOR process consists of four dehydrogenation steps of ethanol leading to the generation of CH2CO species followed by two competitive reaction pathways, i.e., a C-O bond cleavage to poisoning species (e.g., CHC) and the surface diffusion of CH2CO leading to CO2. Furthermore, our studies show that for all CHxCOy (x = 1, 2, or 3 and y = 0 or 1) species, only when the C and O atoms (or two C atoms) bind to two different surface Ir atoms can the C-C/C-O bond cleavage occur. This work highlights the essential roles of adsorption structure and diffusion of CH2CO for the complete EOR and serves as a benchmark for the future investigation of the electronic and solvent effects.Pt-Ir-based alloy electrocatalysts have shown encouraging catalytic performance on the EOR in direct ethanol fuel cells. Nevertheless, designing a suitably qualified EOR electrocatalyst remains challenging because of several convoluted factors (e.g., C1 species poisoning, acetate acid formation, and C-C bond splitting). To understand the relationship between the EOR performance and the type of catalysts, we model three kinds of (100)-exposed Pt-Ir layered catalysts and perform density functional theory (DFT) calculations to explore 58 elementary reactions of the EOR over three catalyst surfaces. According to the calculated activation energies and reaction energies, we mapped out the reaction mechanisms for EOR on different catalysts, indicating corresponding rate-limiting steps (RLSs) of the complete EOR. We demonstrated that the C-O coupling/decoupling ability of the catalyst surface plays a leading role in the overall EOR performance because a perfect complete EOR not only has to avoid some C-O coupling reactions (e.g., CH¬3CO+OH→CH3COOH) but also needs to promote some C-O coupling reactions (e.g., CO+O→CO2). We further illustrated that Pt and Ir exhibit excellent C-O coupling and decoupling abilities, respectively, implying that modifying the compositions and structures of Pt-Ir catalysts is a promising way to achieve the complete EOR. Furthermore, the Ir@Pt(100) surface (Ir monolayer over Pt(100) surface) with a Pt-doped active site possesses the most significant potential on EOR, which could impede the acetate acid formation and facilitate the CO2 formation simultaneously. This work highlights the role of tuning the C-O coupling/decoupling ability of electrocatalyst in EOR activity, providing a new strategy for designing and selecting the EOR electrocatalyst. The solvent effect has always been a non-negligible factor for aqueous reactions. In computational chemistry, researchers have been looking for a compromise between computational efficiency and the rationality of solvent models to mimic the solvent environment. In this work, I investigated the ethanol dehydrogenation and C-C bond cleavages of EOR over Ir(100)using both implicit and explicit solvation models. The implicit model exhibited little impact on the adsorbates without the hydroxyl group, whereas the explicit model can reasonably describe the system’s hydrogen bonding and van der Waals interaction. This solvent effect study showed how different solvent models affected the elementary reactions geometrically and energetically.

Semiconductor nanostructures are currently an active area of research, especially in the field of photovoltaics as they will play a major role in next generation solar devices that break the current theoretical limit for light-to-current conversion. For instance, the efficiency of the nanostructure-based solar cells can be increased due to carrier multiplication, or multiple exciton generation (MEG) process, where absorption of a single energetic photon results in the generation of several charge carriers. In order to design nanostructures with the desired properties, a detailed theoretical approach for studying photoexcited state processes is necessary. The approach developed in this work is based on many-body perturbation theory (MBPT) and the Boltzmann transport equation (BE) in combination with density functional theory (DFT) in order to compute quantum efficiency (QE). Conclusions about QE are made after studying all the major relaxation channels in a photoexcited system, such as exciton-to-biexciton decays, biexciton recombination and phonon-mediated exciton relaxation. In all calculations, excitonic effects have been included by solving the Bethe-Salpeter equation (BSE). Then, by including excitons in the MBPT calculations, the exciton-to- biexciton rates R1→2 as well as the biexciton-to-exciton rates R2→1 are computed by taking into account the singlet fission (SF) process. The methods developed here have been applied to various semiconductor nanostructures such as pristine chiral (6,2), (6,5) and (10,5) and functionalized (6,2) SWCNTs. We predict efficient MEG in the (6,2) and (6,5) SWCNTs within the solar spectrum range starting at the 2Eg energy threshold and with QE reaching ~ 1:6 at about 3Eg, where Eg is the electronic gap. Also, methods for MEG rates calculations have been improved by taking into account exciton-exciton interactions in the intermediate biexciton state, where results show a small (~ 40 meV) red-shift in the biexciton density of states. Finally, the MEG-BE technique is applied in studying charge transfer. Charge transfer has been studied in a doped silicon quantum dot (QD) - functionalized SWCNT system where it was found that an initial excitation localized on either the QD or CNT evolves into a transient CT state. / National Science Foundation (NSF CHE-1413614)