Electrically tunable resonant scattering in fluorinated bilayer graphene

Adatom-decorated graphene offers a promising new path towards spintronics in the ultrathin limit. We combine experiment and theory to investigate the electronic properties of dilutely fluorinated bilayer graphene, where the fluorine adatoms covalently bond to the top graphene layer. We show that fluorine adatoms give rise to resonant impurity states near the charge neutrality point of the bilayer, leading to strong scattering of charge carriers and hopping conduction inside a field-induced band gap. Remarkably, the application of an electric field across the layers is shown to tune the resonant scattering amplitude from fluorine adatoms by nearly twofold. The experimental observations are well explained by a theoretical analysis combining Boltzmann transport equations and fully quantum-mechanical methods. This paradigm can be generalized to many bilayer graphene-adatom materials, and we envision that the realization of electrically tunable resonance may be a key advantage in graphene-based spintronic devices.

The nature of the Cr-C bond: direct estimation of aromaticity in Fischer carbenes

Report for the scientific sojourn at the the Philipps-Universität Marburg, Germany, from september to december 2007. For the first, we employed the Energy-Decomposition Analysis (EDA) to investigate aromaticity on Fischer carbenes as it is related through all the reaction mechanisms studied in my PhD thesis. This powerful tool, compared with other well-known aromaticity indices in the literature like NICS, is useful not only for quantitative results but also to measure the degree of conjugation or hyperconjugation in molecules. Our results showed for the annelated benzenoid systems studied here, that electron density is more concentrated on the outer rings than in the central one. The strain-induced bond localization plays a major role as a driven force to keep the more substituted ring as the less aromatic. The discussion presented in this work was contrasted at different levels of theory to calibrate the method and ensure the consistency of our results. We think these conclusions can also be extended to arene chemistry for explaining aromaticity and regioselectivity reactions found in those systems.In the second work, we have employed the Turbomole program package and density-functionals of the best performance in the state of art, to explore reaction mechanisms in the noble gas chemistry. Particularly, we were interested in compounds of the form H--Ng--Ng--F (where Ng (Noble Gas) = Ar, Kr and Xe) and we investigated the relative stability of these species. Our quantum chemical calculations predict that the dixenon compound HXeXeF has an activation barrier for decomposition of 11 kcal/mol which should be large enough to identify the molecule in a low-temperature matrix. The other noble gases present lower activation barriers and therefore are more labile and difficult to be observable systems experimentally.

Effect of a transverse magnetic field on resonant magnetization tunneling in high-spin molecules

The recent observation of steps at regular intervals of magnetic field in the hysteresis loops of oriented crystals of the spin-10 molecular magnet Mn12O12(CH3COO)16(H2O)4 has been attributed to resonant tunneling between spin states. Here, we investigate the effect on the relaxation rate of applying the magnetic field at an angle with respect to the easy axis of magnetization. We find that the position of the resonances is independent of the transverse component of the field, and is determined solely by the longitudinal component. On the other hand, a transverse field significantly increases the relaxation rate, both on and off resonance. We discuss classical and quantum mechanical interpretations of this effect

Generalized adiabatic invariance

In this paper we find the quantities that are adiabatic invariants of any desired order for a general slowly time-dependent Hamiltonian. In a preceding paper, we chose a quantity that was initially an adiabatic invariant to first order, and sought the conditions to be imposed upon the Hamiltonian so that the quantum mechanical adiabatic theorem would be valid to mth order. [We found that this occurs when the first (m - 1) time derivatives of the Hamiltonian at the initial and final time instants are equal to zero.] Here we look for a quantity that is an adiabatic invariant to mth order for any Hamiltonian that changes slowly in time, and that does not fulfill any special condition (its first time derivatives are not zero initially and finally).

Rigorous characterization of oxygen vacancies in ionic oxides

Charged and neutral oxygen vacancies in the bulk and on perfect and defective surfaces of MgO are characterized as quantum-mechanical subsystems chemically bonded to the host lattice and containing most of the charge left by the removed oxygens. Attractors of the electron density appear inside the vacancy, a necessary condition for the existence of a subsystem according to the atoms in molecules theory. The analysis of the electron localization function also shows attractors at the vacancy sites, which are associated to a localization basin shared with the valence domain of the nearest oxygens. This polyatomic superanion exhibits chemical trends guided by the formal charge and the coordination of the vacancy. The topological approach is shown to be essential to understand and predict the nature and chemical reactivity of these objects. There is not a vacancy but a coreless pseudoanion that behaves as an activated host oxygen.

Ab initio study of the charge order and Zener polaron formation in half-doped manganites

The character of the electronic ground state of La0.5Ca0.5MnO3 has been addressed with quantum chemical calculations on large embedded clusters. We find a charge ordered state for the crystal structure reported by Radaelli et al. [Phys. Rev. B 55, 3015 (1997)] and Zener polaron formation in the crystal structure with equivalent Mn sites proposed by Daoud-Aladine et al. [Phys. Rev. Lett. 89, 097205 (2002)]. Important O to Mn charge transfer effects are observed for the Zener polaron.

Diradicals acting through diamagnetic phenylene vinylene bridges: Raman spectroscopy as a probe to characterize spin delocalization

We present a complete Raman spectroscopic study in two structurally well-defined diradical species of different lengths incorporating oligo p-phenylene vinylene bridges between two polychlorinated triphenylmethyl radical units, a disposition that allows sizeable conjugation between the two radicals through and with the bridge. The spectroscopic data are interpreted and supported by quantum chemical calculations. We focus the attention on the Raman frequency changes, interpretable in terms of: (i) bridge length (conjugation length); (ii) bridge conformational structure; and (iii) electronic coupling between the terminal radical units with the bridge and through the bridge, which could delineate through-bond spin polarization, or spin delocalization. These items are addressed by using the"oligomer approach" in conjunction with pressure and temperature dependent Raman spectroscopic data. In summary, we have attempted to translate the well-known strategy to study the electron (charge) structure of π−conjugated molecules by Raman spectroscopy to the case of electron (spin) interactions via the spin delocalization mechanism.

Model of black hole evolution

We investigate a model where the quantum dynamics of black hole evaporation is determined by imposing a boundary on the apparent horizon with suitable boundary conditions. An unconventional scenario for the evolution emerges: only an insignificant fraction of energy of order (mG)-1 is radiated out; the outgoing wave carries a very small part of the quantum-mechanical information of the collapsed body, the bulk of the information remaining in the final stable black hole geometry.

CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.

Very large molecular systems can be calculated with the so called CNDOL approximate Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term named CNDOL/21 shows great consistency and easier SCF convergence when used together with an appropriate function for charge repulsion energies that is derived from traditional formulas. It is possible to obtain a priori molecular orbitals and electron excitation properties after the configuration interaction of single excited determinants with reliability, maintaining interpretative possibilities even being a simplified Hamiltonian. Tests with some unequivocal gas phase maxima of simple molecules (benzene, furfural, acetaldehyde, hexyl alcohol, methyl amine, 2,5 dimethyl 2,4 hexadiene, and ethyl sulfide) ratify the general quality of this approach in comparison with other methods. The calculation of large systems as porphine in gas phase and a model of the complete retinal binding pocket in rhodopsin with 622 basis functions on 280 atoms at the quantum mechanical level show reliability leading to a resulting first allowed transition in 483 nm, very similar to the known experimental value of 500 nm of "dark state." In this very important case, our model gives a central role in this excitation to a charge transfer from the neighboring Glu(-) counterion to the retinaldehyde polyene chain. Tests with gas phase maxima of some important molecules corroborate the reliability of CNDOL/2 Hamiltonians.

Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant.

Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies.

Espectro infravermelho e análise conformacional do composto 3-fenil-2-oxo-1,2,3-oxatiazolidina

The infrared (IR) spectra of the four distict conformers located on the multidimensional potential energy surface (PES) for the 3-phenyl-1,2,3-oxathiazolidine 2-oxide compound have been calculated using the semiempirical quantum-mechanical method PM3. The band spectra are reported and compared directly with the experimental spectrum. The IR intensities are shown to be much more sensitive to conformational changes than the vibrational frequencies and so, the theoretical analysis of the IR spectrum can be used as a tool for helping in the elucidation of the structure of heterocyclic compounds.

Análise conformacional de modelos de lignina

The conformational equilibrium for two 5,5' biphenyl lignin models have been analyzed using a quantum mechanical semiempirical method. The gas phase and solution structures are discussed based on the NMR and X-ray experimental data. The results obtained showed that the observed conformations are solvent-dependent, being the geometries and the thermodynamic properties correlated with the experimental information. This study shows how a systematic theoretical conformational analysis can help to understand chemical processes at a molecular level.

Estudo QSPR sobre os coeficientes de partição: descritores mecânico-quânticos e análise multivariada

Quantum chemistry and multivariate analysis were used to estimate the partition coefficients between n-octanol and water for a serie of 188 compounds, with the values of the q 2 until 0.86 for crossvalidation test. The quantum-mechanical descriptors are obtained with ab initio calculation, using the solvation effects of the Polarizable Continuum Method. Two different Hartree-Fock bases were used, and two different ways for simulating solvent cavity formation. The results for each of the cases were analised, and each methodology proposed is indicated for particular case.

NCT: pacote de tratamento de coordenadas normais (versão 7)

A new version of the normal coordinate analysis package NCT is presented. The upgrade was mainly devised to enable the NCT package to manipulate easily the Hessian matrix evaluated by quantum chemical calculations. Program codes were almost wholly rewritten to be more efficient with GNU Fortran77, or g77, and compiled under FreeBSD and MS-DOS with the DJGPP implementation. Three typical usages of the program package are presented by giving the related input and output files. Functionality of the programs was carefully and satisfactorily checked for some sample calculations.

Análise estrutural de ciclodextrinas: um estudo comparativo entre métodos teóricos clássicos e quânticos

In the present work, we analyzed the accuracy of distinct theoretical methods to reproduce the solid state structures of cyclodextrins. The a, b and g-cyclodextrins (CD) were considered and also their hydrates with included water molecules: a-CD.2H2O, b-CD.10H2O and g-CD.12H2O. The geometries were fully optimized using Molecular Mechanics (MM2), semiempirical (AM1 and PM3) and ab initio (HF/3-21G) methods and quantitatively compared with experimental data from X ray diffraction. The results obtained from the classical MM2 method were in best agreement with the experiment. The semiempirical and ab initio structures were also in satisfactory accordance with the experimental data. In general, the PM3 method was found to be more suitable than the AM1 to describe the CD geometries, mainly when the intramolecular hydrogen bonds are considered.