Light emission and current rectification in a molecular device: Experiment and theory

We have investigated optical and transport properties of the molecular structure 2,3,4,5-tetraphenyl-1-phenylethynyl-cyclopenta-2,4-dienol experimentally and theoretically. The optical spectrum was calculated using Hartree-Fock-intermediate neglect of differential overlap-configuration interaction model. The experimental photoluminescence spectrum showed a peak around 470nm which was very well described by the modeling. Electronic transport measurements showed a diode-like effect with a strong current rectification. A phenomenological microscopic model based on non-equilibrium Green's function technique was proposed and a very good description electronic transport was obtained. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4767457]

Mathematical modeling and analysis of the particle interactions in the direct filtration using the colloidal theory

This work used the colloidal theory to describe forces and energy interactions of colloidal complexes in the water and those formed during filtration run in direct filtration. Many interactions of particle energy profiles between colloidal surfaces for three geometries are presented here in: spherical, plate and cylindrical; and four surface interactions arrangements: two cylinders, two spheres, two plates and a sphere and a plate. Two different situations were analyzed, before and after electrostatic destabilization by action of the alum sulfate as coagulant in water studies samples prepared with kaolin. In the case were used mathematical modeling by extended DLVO theory (from the names: Derjarguin-Landau-Verwey-Overbeek) or XDLVO, which include traditional approach of the electric double layer (EDL), surfaces attraction forces or London-van der Waals (LvdW), esteric forces and hydrophobic forces, additionally considering another forces in colloidal system, like molecular repulsion or Born Repulsion and Acid-Base (AB) chemical function forces from Lewis.

Electrostatic potentials and polarization effects in proton-molecule interactions by means of multipoles from the quantum theory of atoms in molecules

Some atomic multipoles (charges, dipoles and quadrupoles) from the Quantum Theory of Atoms in Molecules (QTAIM) and CHELPG charges are used to investigate interactions between a proton and a molecule (F2, Cl2, BF, AlF, BeO, MgO, LiH, H2CO, NH3, PH3, BF3, and CO2). Calculations were done at the B3LYP/6-311G(3d,3p) level. The main aspect of this work is the investigation of polarization effects over electrostatic potentials and atomic multipoles along a medium to long range of interaction distances. Large electronic charge fluxes and polarization changes are induced by a proton mainly when this positive particle approaches the least electronegative atom of diatomic heteronuclear molecules. The search for simple equations to describe polarization on electrostatic potentials from QTAIM quantities resulted in linear relations with r-4 (r is the interaction distance) for many cases. Moreover, the contribution from atomic dipoles to these potentials is usually the most affected contribution by polarization what reinforces the need for these dipoles to a minimal description of purely electrostatic interactions. Finally, CHELPG charges provide a description of polarization effects on electrostatic potentials that is in disagreement with physical arguments for certain of these molecules. (c) 2012 Wiley Periodicals, Inc.

Interactions between 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid and gamma-Al2O3 (100) surface calculated by density functional theory

The main aim of this work is to investigate the 1-butyl-3-methylimidazolium tetrafluoroborate ([C4C1Im]+[BF4]-) ionic liquid (IL) adsorption on the gamma-Al2O3 (100) by density functional theory calculations to try to rationalize the adsorption as an electrostatic phenomenon. Optimized geometries and interaction energies of IL one-monolayer on the gamma-Al2O3 were obtained on high surface coverage (one cationanion pair per 94.96 nm2). A study of dispersion force was made to estimate its contribution to the adsorption. Overall, the process is ruled by electrostatic interaction between ions and surface. Adsorption of the anion [BF4]- and cation [C4C1Im]+ was also studied by Bader charge analysis and charge density difference for supported and unsupported situations. It is suggested that the IL ions have their charges maintained with significant anion cloud polarization inward to the acid aluminum sites. (c) 2012 Wiley Periodicals, Inc.

The search for a potentially new molecular species, SiAs: A theoretical contribution

Electronic states of a new molecular species, SiAs, correlating with the three lowest dissociation channels are characterized at a high-level of theory using the CASSCF/MRCI approach along with quintuple-xi quality basis sets. This characterization includes potential energy curves, vibrational energy levels, spectroscopic parameters, dipole and transition dipole moment functions, transition probabilities, and radiative lifetimes. For the ground state (X-2 Pi), an assessment of spin-orbit effects and the interaction with the close-lying A(2)Sigma(+) state is also reported. Similarities and differences with other isovalent species such as SiP and CAs are also discussed.

Structure and electronic properties of hydrated mesityl oxide: a sequential quantum mechanics/molecular mechanics approach

The hydration of mesityl oxide (MOx) was investigated through a sequential quantum mechanics/molecular mechanics approach. Emphasis was placed on the analysis of the role played by water in the MOx syn-anti equilibrium and the electronic absorption spectrum. Results for the structure of the MOx-water solution, free energy of solvation and polarization effects are also reported. Our main conclusion was that in gas-phase and in low-polarity solvents, the MOx exists dominantly in syn-form and in aqueous solution in anti-form. This conclusion was supported by Gibbs free energy calculations in gas phase and in-water by quantum mechanical calculations with polarizable continuum model and thermodynamic perturbation theory in Monte Carlo simulations using a polarized MOx model. The consideration of the in-water polarization of the MOx is very important to correctly describe the solute-solvent electrostatic interaction. Our best estimate for the shift of the pi-pi* transition energy of MOx, when it changes from gas-phase to water solvent, shows a red-shift of -2,520 +/- 90 cm(-1), which is only 110 cm(-1) (0.014 eV) below the experimental extrapolation of -2,410 +/- 90 cm(-1). This red-shift of around -2,500 cm(-1) can be divided in two distinct and opposite contributions. One contribution is related to the syn -> anti conformational change leading to a blue-shift of similar to 1,700 cm(-1). Other contribution is the solvent effect on the electronic structure of the MOx leading to a red-shift of around -4,200 cm(-1). Additionally, this red-shift caused by the solvent effect on the electronic structure can by composed by approximately 60 % due to the electrostatic bulk effect, 10 % due to the explicit inclusion of the hydrogen-bonded water molecules and 30 % due to the explicit inclusion of the nearest water molecules.

The Role of Molecular Conformation and Polarizable Embedding for One- and Two-Photon Absorption of Disperse Orange 3 in Solution

Solvent effects on the one- and two-photon absorption (IPA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

Adsorption of NO on the Rh-13, Pd-13, Ir-13, and Pt-13 Clusters: A Density Functional Theory Investigation

The adsorption of NO on transition-metal (TM) surfaces has been widely studied by experimental and theoretical techniques; however, our atomistic understanding of the interaction of nitrogen monoxide (NO) with small TM clusters is far from satisfactory, which compromises a deep understanding of real catalyst devices. In this study, we report a density functional theory study of the adsorption properties of NO on the TM13 (TM = Rh, Pd, Ir, Pt) clusters employing the projected augmented wave method. We found that the interaction of NO with TM13 is much more complex than that for NO/TM(111). In particular, for low symmetry TM13 clusters, there is a strong rearrangement of the electronic charge density upon NO adsorption and, as a consequence, the adsorption energy shows a very complex dependence even for adsorption sites with the same local effective coordination. We found a strong enhancement of the binding energy of NO to the TM13 clusters compared with the TM(111) surfaces, as the antibonding NO states are not occupied for NO/TM13, and the general relationship based on the d-band model between adsorption energy and the center of gravity of the occupied d-states does not hold for the studied TM13 clusters, in particular, for clusters with low symmetry. In contrast with the adsorption energy trends, the geometric NO/TM13 parameters and the vibrational N-O frequencies for different coordination sites follow the same trend as for the respective TM(111) surfaces, while the changes in the frequencies between different surfaces and TM13 clusters reflect the strong NO-TM13 interaction.

Density Functional Theory (DFT) Study of Edaravone Derivatives as Antioxidants

Quantum chemical calculations at the B3LYP/6-31G* level of theory were employed for the structure-activity relationship and prediction of the antioxidant activity of edaravone and structurally related derivatives using energy (E), ionization potential (IP), bond dissociation energy (BDE), and stabilization energies(Delta E-iso). Spin density calculations were also performed for the proposed antioxidant activity mechanism. The electron abstraction is related to electron-donating groups (EDG) at position 3, decreasing the IP when compared to substitution at position 4. The hydrogen abstraction is related to electron-withdrawing groups (EDG) at position 4, decreasing the BDECH when compared to other substitutions, resulting in a better antioxidant activity. The unpaired electron formed by the hydrogen abstraction from the C-H group of the pyrazole ring is localized at 2, 4, and 6 positions. The highest scavenging activity prediction is related to the lowest contribution at the carbon atom. The likely mechanism is related to hydrogen transfer. It was found that antioxidant activity depends on the presence of EDG at the C-2 and C-4 positions and there is a correlation between IP and BDE. Our results identified three different classes of new derivatives more potent than edaravone.

Platinum-Based Nanoalloys PtnTM55-n (TM=Co, Rh, Au): A Density Functional Theory Investigation

Structural and electronic properties of the PtnTM55-n (TM = Co, Rh, Au) nanoalloys are investigated using density functional theory within the generalized gradient approximation and employing the all-electron projected augmented wave method. For TM = Co and Rh, the excess energy, which measures the relative energy stability of the nanoalloys, is negative for all Pt compositions. We found that the excess energy has similar values for a wide range of Pt compositions, i.e., n = 20-42 and n = 28-42 for Co and Rh, respectively, with the core shell icosahedron-like configuration (n = 42) being slightly more stable for both Co and Rh systems because of the larger release of the strain energy due to the smaller atomic size of the Co and Rh atoms. For TM = Au, the excess energy is positive for all compositions, except for n = 13, which is energetically favorable due to the formation of the core-shell structure (Pt in the core and Au atoms at the surface). Thus, our calculations confirm that the formation of core-shell structures plays an important role to increase the stability of nanoalloys. The center of gravity of the occupied d-states changes almost linearly as a function of the Pt composition, and hence, based on the d-band model, the magnitude of the adsorption energy of an adsorbate can be tuned by changing the Pt composition. The magnetic moments of PtnCo55-n decrease almost linearly as a function of the Pt composition; however, the same does not hold for PtRh and PtAu. We found an enhancement of the magnetic moments of PtRh by a few times by increasing Pt composition, which we explain by the compression effects induced by the large size of the Pt atoms compared with the Rh atoms.

Recoupled separated-local-field experiments and applications to study intermediate-regime molecular motions

A specific separated-local-field NMR experiment, dubbed Dipolar-Chemical-Shift Correlation (DIPSHIFT) is frequently used to study molecular motions by probing reorientations through the changes in XH dipolar coupling and T-2. In systems where the coupling is weak or the reorientation angle is small, a recoupled variant of the DIPSHIFT experiment is applied, where the effective dipolar coupling is amplified by a REDOR-like pi-pulse train. However, a previously described constant-time variant of this experiment is not sensitive to the motion-induced T-2 effect, which precludes the observation of motions over a large range of rates ranging from hundreds of Hz to around a MHz. We present a DIPSHIFT implementation which amplifies the dipolar couplings and is still sensitive to T-2 effects. Spin dynamics simulations, analytical calculations and experiments demonstrate the sensitivity of the technique to molecular motions, and suggest the best experimental conditions to avoid imperfections. Furthermore, an in-depth theoretical analysis of the interplay of REDOR-like recoupling and proton decoupling based on Average-Hamiltonian Theory was performed, which allowed explaining the origin of many artifacts found in literature data. (C) 2012 Elsevier Inc. All rights reserved.

Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera

Abstract Background In honeybees, differential feeding of female larvae promotes the occurrence of two different phenotypes, a queen and a worker, from identical genotypes, through incremental alterations, which affect general growth, and character state alterations that result in the presence or absence of specific structures. Although previous studies revealed a link between incremental alterations and differential expression of physiometabolic genes, the molecular changes accompanying character state alterations remain unknown. Results By using cDNA microarray analyses of >6,000 Apis mellifera ESTs, we found 240 differentially expressed genes (DEGs) between developing queens and workers. Many genes recorded as up-regulated in prospective workers appear to be unique to A. mellifera, suggesting that the workers' developmental pathway involves the participation of novel genes. Workers up-regulate more developmental genes than queens, whereas queens up-regulate a greater proportion of physiometabolic genes, including genes coding for metabolic enzymes and genes whose products are known to regulate the rate of mass-transforming processes and the general growth of the organism (e.g., tor). Many DEGs are likely to be involved in processes favoring the development of caste-biased structures, like brain, legs and ovaries, as well as genes that code for cytoskeleton constituents. Treatment of developing worker larvae with juvenile hormone (JH) revealed 52 JH responsive genes, specifically during the critical period of caste development. Using Gibbs sampling and Expectation Maximization algorithms, we discovered eight overrepresented cis-elements from four gene groups. Graph theory and complex networks concepts were adopted to attain powerful graphical representations of the interrelation between cis-elements and genes and objectively quantify the degree of relationship between these entities. Conclusion We suggest that clusters of functionally related DEGs are co-regulated during caste development in honeybees. This network of interactions is activated by nutrition-driven stimuli in early larval stages. Our data are consistent with the hypothesis that JH is a key component of the developmental determination of queen-like characters. Finally, we propose a conceptual model of caste differentiation in A. mellifera based on gene-regulatory networks.

Applying many-body expansion aiming to make ab in initio molecular dynamics more efficient

In this present work we present a methodology that aims to apply the many-body expansion to decrease the computational cost of ab initio molecular dynamics, keeping acceptable accuracy on the results. We implemented this methodology in a program which we called ManBo. In the many-body expansion approach, we partitioned the total energy E of the system in contributions of one body, two bodies, three bodies, etc., until the contribution of the Nth body [1-3]: E = E1 + E2 + E3 + …EN. The E1 term is the sum of the internal energy of the molecules; the term E2 is the energy due to interaction between all pairs of molecules; E3 is the energy due to interaction between all trios of molecules; and so on. In Manbo we chose to truncate the expansion in the contribution of two or three bodies, both for the calculation of the energy and for the calculation of the atomic forces. In order to partially include the many-body interactions neglected when we truncate the expansion, we can include an electrostatic embedding in the electronic structure calculations, instead of considering the monomers, pairs and trios as isolated molecules in space. In simulations we made we chose to simulate water molecules, and use the Gaussian 09 as external program to calculate the atomic forces and energy of the system, as well as reference program for analyzing the accuracy of the results obtained with the ManBo. The results show that the use of the many-body expansion seems to be an interesting approach for reducing the still prohibitive computational cost of ab initio molecular dynamics. The errors introduced on atomic forces in applying such methodology are very small. The inclusion of an embedding electrostatic seems to be a good solution for improving the results with only a small increase in simulation time. As we increase the level of calculation, the simulation time of ManBo tends to largely decrease in relation to a conventional BOMD simulation of Gaussian, due to better scalability of the methodology presented. References [1] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 3, 46 (2007). [2] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 4, 1 (2008). [3] R. Rivelino, P. Chaudhuri and S. Canuto; J. Chem. Phys., 118, 10593 (2003).