Infrared absorption spectra, radiative efficiencies, and global warming potentials of perfluorocarbons: Comparison between experiment and theory

Experimentally and theoretically determined infrared spectra are reported for a series of straight-chain perfluorocarbons: C2F6, C3F8, C4F10, C5F12, C6F14, and C8F18. Theoretical spectra were determined using both density functional (DFT) and ab initio methods. Radiative efficiencies (REs) were determined using the method of Pinnock et al. (1995) and combined with atmospheric lifetimes from the literature to determine global warming potentials (GWPs). Theoretically determined absorption cross sections were within 10% of experimentally determined values. Despite being much less computationally expensive, DFT calculations were generally found to perform better than ab initio methods. There is a strong wavenumber dependence of radiative forcing in the region of the fundamental C-F vibration, and small differences in wavelength between band positions determined by theory and experiment have a significant impact on the REs. We apply an empirical correction to the theoretical spectra and then test this correction on a number of branched chain and cyclic perfluoroalkanes. We then compute absorption cross sections, REs, and GWPs for an additional set of perfluoroalkenes.

Nonmonotonic Magnetic Susceptibility of Dipolar Hard-Spheres at Low Temperature and Density

We investigate, via numerical simulations, mean field, and density functional theories, the magnetic response of a dipolar hard sphere fluid at low temperatures and densities, in the region of strong association. The proposed parameter-free theory is able to capture both the density and temperature dependence of the ring-chain equilibrium and the contribution to the susceptibility of a chain of generic length. The theory predicts a nonmonotonic temperature dependence of the initial (zero field) magnetic susceptibility, arising from the competition between magnetically inert particle rings and magnetically active chains. Monte Carlo simulation results closely agree with the theoretical findings. DOI: 10.1103/PhysRevLett.110.148306

Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

We address the challenges of treating polarization and covalent interactions in docking by developing a hybrid quantum mechanical/molecular mechanical (QM/MM) scoring function based on the semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) method and the CHARMM force field. To benchmark this scoring function within the EADock DSS docking algorithm, we created a publicly available dataset of high-quality X-ray structures of zinc metalloproteins ( http://www.molecular-modelling.ch/resources.php ). For zinc-bound ligands (226 complexes), the QM/MM scoring yielded a substantially improved success rate compared to the classical scoring function (77.0% vs 61.5%), while, for allosteric ligands (55 complexes), the success rate remained constant (49.1%). The QM/MM scoring significantly improved the detection of correct zinc-binding geometries and improved the docking success rate by more than 20% for several important drug targets. The performance of both the classical and the QM/MM scoring functions compare favorably to the performance of AutoDock4, AutoDock4Zn, and AutoDock Vina.

Etudes ab initio des effets de la température sur le spectre optique des semi-conducteurs

Thèse réalisée en cotutelle avec l'Université Catholique de Louvain (Belgique)

Radiative efficiencies and global warming potentials using theoretically determined absorption cross-sections for several hydrofluoroethers (HFEs) and hydrofluoropolyethers (HFPEs)

Integrated infrared cross-sections and wavenumber positions for the vibrational modes of a range of hydrofluoroethers (HFEs) and hydrofluoropolyethers (HFPEs) have been calculated. Spectra were determined using a density functional method with an empirically derived correction for the wavenumbers of band positions. Radiative efficiencies (REs) were determined using the Pinnock et al. method and were used with atmospheric lifetimes from the literature to determine global warming potentials (GWPs). For the HFEs and the majority of the molecules in the HG series HFPEs, theoretically determined absorption cross-sections and REs lie within ca. 10% of those determined using measured spectra. For the larger molecules in the HG series and the HG′ series of HFPEs, agreement is less good, with theoretical values for the integrated cross-sections being up to 35% higher than the experimental values; REs are up to 45% higher. Our method gives better results than previous theoretical approaches, because of the level of theory chosen and, for REs, because an empirical wavenumber correction derived for perfluorocarbons is effective in predicting the positions of C–F stretching frequencies at around 1250 cm−1 for the molecules considered here.

First-principles calculation of the AlAs/GaAs interface band structure using a self-energy-corrected local density approximation

We apply a self-energy-corrected local density approximation (LDA) to obtain corrected bulk band gaps and to study the band offsets of AlAs grown on GaAs (AlAs/GaAs). We also investigate the Al(x)Ga(1-x)As/GaAs alloy interface, commonly employed in band gap engineering. The calculations are fully ab initio, with no adjustable parameters or experimental input, and at a computational cost comparable to traditional LDA. Our results are in good agreement with experimental values and other theoretical studies. Copyright (C) EPLA, 2011

Dynamical self-stabilization of the Mott insulator: Time evolution of the density and entanglement entropy of out-of-equilibrium cold fermion gases

The time evolution of the out-of-equilibrium Mott insulator is investigated numerically through calculations of space-time-resolved density and entropy profiles resulting from the release of a gas of ultracold fermionic atoms from an optical trap. For adiabatic, moderate and sudden switching-off of the trapping potential, the out-of-equilibrium dynamics of the Mott insulator is found to differ profoundly from that of the band insulator and the metallic phase, displaying a self-induced stability that is robust within a wide range of densities, system sizes and interaction strengths. The connection between the entanglement entropy and changes of phase, known for equilibrium situations, is found to extend to the out-of-equilibrium regime. Finally, the relation between the system`s long time behavior and the thermalization limit is analyzed. Copyright (C) EPLA, 2011

Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method

There is a continuous search for theoretical methods that are able to describe the effects of the liquid environment on molecular systems. Different methods emphasize different aspects, and the treatment of both the local and bulk properties is still a great challenge. In this work, the electronic properties of a water molecule in liquid environment is studied by performing a relaxation of the geometry and electronic distribution using the free energy gradient method. This is made using a series of steps in each of which we run a purely molecular mechanical (MM) Monte Carlo Metropolis simulation of liquid water and subsequently perform a quantum mechanical/molecular mechanical (QM/MM) calculation of the ensemble averages of the charge distribution, atomic forces, and second derivatives. The MP2/aug-cc-pV5Z level is used to describe the electronic properties of the QM water. B3LYP with specially designed basis functions are used for the magnetic properties. Very good agreement is found for the local properties of water, such as geometry, vibrational frequencies, dipole moment, dipole polarizability, chemical shift, and spin-spin coupling constants. The very good performance of the free energy method combined with a QM/MM approach along with the possible limitations are briefly discussed.

Alternative derivative expansion in Functional RG and application

We give a brief review of the Functional Renormalization method in quantum field theory, which is intrinsically non perturbative, in terms of both the Polchinski equation for the Wilsonian action and the Wetterich equation for the generator of the proper verteces. For the latter case we show a simple application for a theory with one real scalar field within the LPA and LPA' approximations. For the first case, instead, we give a covariant "Hamiltonian" version of the Polchinski equation which consists in doing a Legendre transform of the flow for the corresponding effective Lagrangian replacing arbitrary high order derivative of fields with momenta fields. This approach is suitable for studying new truncations in the derivative expansion. We apply this formulation for a theory with one real scalar field and, as a novel result, derive the flow equations for a theory with N real scalar fields with the O(N) internal symmetry. Within this new approach we analyze numerically the scaling solutions for N=1 in d=3 (critical Ising model), at the leading order in the derivative expansion with an infinite number of couplings, encoded in two functions V(phi) and Z(phi), obtaining an estimate for the quantum anomalous dimension with a 10% accuracy (confronting with Monte Carlo results).

Structural Analysis of alpha-Fetoprotein (AFP)-like Peptides with Anti-Breast-Cancer Properties

The abundance of alpha-fetoprotein (AFP), a natural protein produced by the fetal yolk sac during pregnancy, correlates with lower incidence of estrogen receptor positive (ER+) breast cancer. The pharmacophore region of AFP has been narrowed down to a four amino acid (AA) region in the third domain of the 591 AA peptide. Our computational study focuses on a 4-mer segment consisting of the amino acids threonine-proline-valine-asparagine (TPVN). We have run replica exchange molecular dynamics (REMD) simulations and used 120 configurational snapshots from the total trajectory as starting configurations for quantum chemical calculations. We optimized structures using semiempirical (PM3, PM6, PM6-D2, PM6-H2, PM6-DH+, PM6-DH2) and density functional methods (TPSS, PBE0, M06-2X). By comparing the accuracy of these methods against RI-MP2 benchmarks, we devised a protocol for calculating the lowest energy conformers of these peptides accurately and efficiently. This protocol screens out high-energy conformers using lower levels of theory and outlines a general method for predicting small peptide structures.

Correlation between Accurate Electron Density and Linear Optical Properties in Amino Acid Derivatives: L-Histidinium Hydrogen Oxalate

The accurate electron density and linear optical properties of L-histidinium hydrogen oxalate are discussed. Two high-resolution single crystal X-ray diffraction experiments were performed and compared with density functional calculations in the solid state as well as in the gas phase. The crystal packing and the hydrogen bond network are accurately investigated using topological analysis based on quantum theory of atoms in molecules, Hirshfeld surface analysis, and electrostatic potential mapping. The refractive indices are computed from couple perturbed Kohn-Sham calculations and measured experimentally. Moreover, distributed atomic polarizabilities are used to analyze the origin of the linear susceptibility in the crystal, in order to separate molecular and intermolecular causes. The optical properties are also correlated with the electron density distribution. This compound also offers the possibility to test the electron density building block approach for material science and different refinement schemes for accurate positions and displacement parameters of hydrogen atoms, in the absence of neutron diffraction data.

Modelos determinístico y probabilístico para la estimación de la carga de nitratos en una cuenca rural

En este trabajo se desarrolló un modelo probabilístico que utiliza la teoría de la función de densidad de probabilidades derivada para estimar la carga media anual de nitratos transportada por el escurrimiento superficial, utilizando una relación funcional entre el escurrimiento y la carga de nitratos. El modelo determinístico hidrológico y de calidad de agua denominado Simulator for Water Resources in Rural Basins - Water Quality (SWRRB-WQ) fue utilizado para estimar la carga de nitratos en el escurrimiento superficial. Este modelo emplea como variable de entrada la precipitación diaria observada en la Estación del Aeropuerto de Olavarría durante el período 1988 a 2002. Para la calibración del modelo se aplicó una nueva metodología que estima la incertidumbre en los valores observados. Ambos modelos probabilístico y determinístico se aplican en una subcuenca rural del arroyo Tapalqué (provincia de Buenos Aires, Argentina) y finalmente se comparan los valores de la carga de nitratos estimados con los dos modelos con las observaciones realizadas en la sección del arroyo motivo de este estudio. Los resultados muestran que la carga media de nitratos obtenida con el modelo probabilístico es del mismo orden de magnitud que los valores medios observados y estimados con el modelo hidrológico y de calidad de agua SWRRB-WQ.

Why H Atom Prefers the On-Top Site and Alkali Metals Favor the Middle Hollow Site on the Basal Plane of Graphite

In this work, the different adsorption properties of H and alkali metal atoms on the basal plane of graphite are studied and compared using a density functional method on the same model chemistry level. The results show that H prefers the on-top site while alkali metals favor the middle hollow site of graphite basal plane due to the unique electronic structures of H, alkali metals, and graphite. H has a higher electronegativity than carbon, preferring to form a covalent bond with C atoms, whereas alkaline metals have lower electronegativity, tending to adsorb on the highest electrostatic potential sites. During adsorption, there are more charges transferred from alkali metal to graphite than from H to graphite.

The Equilibrium Flux Method for the calculation of flows with non-equilbrium chemical reactions

The Equilibrium Flux Method [1] is a kinetic theory based finite volume method for calculating the flow of a compressible ideal gas. It is shown here that, in effect, the method solves the Euler equations with added pseudo-dissipative terms and that it is a natural upwinding scheme. The method can be easily modified so that the flow of a chemically reacting gas mixture can be calculated. Results from the method for a one-dimensional non-equilibrium reacting flow are shown to agree well with a conventional continuum solution. Results are also presented for the calculation of a plane two-dimensional flow, at hypersonic speed, of a dissociating gas around a blunt-nosed body.

An inverse design method for elliptical MRI magnets

An inverse, current density mapping (CDM) method has been developed for the design of elliptical cross-section MRI magnets. The method provides a rapid prototyping system for unusual magnet designs, as it generates a 3D current density in response to a set of target field and geometric constraints. The emphasis of this work is on the investigation of new elliptical coil structures for clinical MRI magnets. The effect of the elliptical aspect ratio on magnet performance is investigated. Viable designs are generated for symmetric, asymmetric and open architecture elliptical magnets using the new method. Clinically relevant attributes such as reduced stray field and large homogeneous regions relative to total magnet length are included in the design process and investigated in detail. The preliminary magnet designs have several novel features.