Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within t...

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

The electronic ground state of a periodic system is usually described in terms of extended Bloch orbitals, but an alternative representation in terms of localized "Wannier functions" was introduced by Gregory Wannier in 1937. The connection between the Bloch and Wannier representations is realized by families of transformations in a continuous space of unitary matrices, carrying a large degree of arbitrariness. Since 1997, methods have been developed that allow one to iteratively transform the extended Bloch orbitals of a first-principles calculation into a unique set of maximally localized Wannier functions, accomplishing the solid-state equivalent of constructing localized molecular orbitals, or "Boys orbitals" as previously known from the chemistry literature. These developments are reviewed here, and a survey of the applications of these methods is presented. This latter includes a description of their use in analyzing the nature of chemical bonding, or as a local probe of phenomena related to electric polarization and orbital magnetization. Wannier interpolation schemes are also reviewed, by which quantities computed on a coarse reciprocal-space mesh can be used to interpolate onto much finer meshes at low cost, and applications in which Wannier functions are used as efficient basis functions are discussed. Finally the construction and use of Wannier functions outside the context of electronic-structure theory is presented, for cases that include phonon excitations, photonic crystals, and cold-atom optical lattices.

Maximally-localized Wannier Functions: Theory and Applications

Microfabrication of graphene devices used in many experimental studies currently relies on the fact that graphene crystallites can be visualized using optical microscopy if prepared on top of Si wafers with a certain thickness of SiO2. The authors study graphene’s visibility and show that it depends strongly on both thickness of SiO2 and light wavelength. They have found that by using monochromatic illumination, graphene can be isolated for any SiO2 thickness, albeit 300nm (the current standard) and, especially, ≈100nm are most suitable for its visual detection. By using a Fresnel-law-based model, they quantitatively describe the experimental data.

/pdf/making-graphene-visible-4fjbh75lug.pdf

Making graphene visible

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

In this paper we briefly review the basic requirements that must be satisfied by any wave function representing many-electron systems. Following that, we examine the conditions under which the classical concepts of molecular structure, chemical structure and chemical bond can be translated into a quantum-mechanical language. Essential to this aim is the utilization of an independent particle model (IPM) for a many-electron system. In spite of the great popularity of the Hartree-Fock (HF) model only Valence-Bond (VB) type wave functions with optimized, singly occupied and non necessarily orthogonal atomic-like orbitals, can provide a quantum-mechanical translation of the classical concepts of chemical structure and chemical bond, although the HF model can still be useful for translating the concept of molecular structure. Finally, a quantum-dynamical-type of analysis allows us to conclude that, from the quantum mechanical point of view, the chemical bond is a consequence of interference effects. From the energetic point of view, the interference effect responsible for the bond formation manifests itself as a reduction of the kinetic energy of the electrons as the bond is formed.

/pdf/the-nature-of-the-chemical-bond-59hipfhmqz.pdf

The nature of the chemical bond

A thermodynamical cycle is proposed to calculate absolute pKa values for a Bronsted acid in aqueous solution. The solvent (water) was represented by a dielectric using the polarizable continuum model (PCM), and the absolute pKa values of some aliphatic carboxylic acids were computed. The results indicate that the proposed methodology seems to be capable of predicting reasonably good absolute pKa values, although in some cases appreciable deviations are observed, which can be related to neglecting the molecular motion contributions (ΔGMm) to the solvation energy (ΔGsolv).

Ab Initio Calculations of Absolute pKa Values in Aqueous Solution I. Carboxylic Acids

A thermodynamical cycle is proposed to calculate absolute pKa values for Bronsted acids in aqueous solution. The polarizable continuum model (PCM) was used to describe the solvent, and absolute pKa values were computed for different classes of organic compounds:  aliphatic alcohols, thiols, and halogenated derivatives of carboxylic aliphatic acids. The model furnishes pKa values in good agreement with the experimental results for some classes of compounds. For the cases where appreciable deviations are observed, we have tried to establish a correlation among the neglected components of ΔGsolv resulting from the model adopted, the level of calculation employed, and the pKa deviations relative to the experimental results.

Ab Initio Calculations of Absolute pKa Values in Aqueous Solution II. Aliphatic Alcohols, Thiols, and Halogenated Carboxylic Acids

In order to simulate the effects of hydrostatic pressure on protein folding/unfolding it is necessary to accurately describe the behavior of the dielectric constant and the density of the solvent (water), in the range of pressures (between 0.1 MPa and 2.0 GPa) and temperatures (below 75 ° C) required for pressure-induced unfolding. A simple equation of the form X = X (T, Pi) + a0 ln (ai+ P)/(ai + Pi) [were X is the property, Pi (in MPa) is the reference pressure and ai are coefficients adjusted to fit experimental values] is proposed to describe both properties as function of pressure, at constant temperatures. The equation reproduces available data for dielectric constant and density of water to an accuracy of 0.1%. Because of its simplicity and accuracy, the proposed equation is useful for simulation studies and for any other problem where the knowledge of those properties as a function of pressure is needed.

/pdf/dielectric-constant-and-density-of-water-as-a-function-of-2hjun3rx8r.pdf

Dielectric constant and density of water as a function of pressure at constant temperature

Ab initio calculations were performed for X+(H2)n clusters [X=Li, Na (n=1–7) and K (n=1–3)]. For n=1–6, the equilibrium geometries correspond to spherically symmetrical distributions of H2 units around the X+. The binding energies and the geometric parameters indicate that the seventh H2 unit opens a new shell of ligands for the cluster with X=Li but not for X=Na.

Marco Antonio Chaer Nascimento

Papers

The nature of the chemical bond

Ab Initio Calculations of Absolute pKa Values in Aqueous Solution I. Carboxylic Acids

Ab Initio Calculations of Absolute pKa Values in Aqueous Solution II. Aliphatic Alcohols, Thiols, and Halogenated Carboxylic Acids

Dielectric constant and density of water as a function of pressure at constant temperature

The effects of the presence of an alkaline atomic cation in a molecular hydrogen environment