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

: 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 the past 30 years, Kohn–Sham density functional theory has emerged as the most popular electronic structure method in computational chemistry. To assess the ever-increasing number of approximate...

Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals

Lung Wa Chung,† W. M. C. Sameera,‡ Romain Ramozzi,‡ Alister J. Page, Miho Hatanaka,‡ Galina P. Petrova, Travis V. Harris,‡,⊥ Xin Li, Zhuofeng Ke, Fengyi Liu, Hai-Bei Li, Lina Ding, and Keiji Morokuma*,‡ †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi 710119, China School of Ocean, Shandong University, Weihai 264209, China School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China

The ONIOM Method and Its Applications

Carbon nanotubes (CNTs) have been proposed and actively explored as multipurpose innovative carriers for drug delivery and diagnostic applications. Their versatile physicochemical features enable the covalent and noncovalent introduction of several pharmaceutically relevant entities and allow for rational design of novel candidate nanoscale constructs for drug development. CNTs can be functionalized with different functional groups to carry simultaneously several moieties for targeting, imaging, and therapy. Among the most interesting examples of such multimodal CNT constructs described in this Account is one carrying a fluorescein probe together with the antifungal drug amphotericin B or fluorescein and the antitumor agent methotrexate. The biological action of the drug in these cases is retained or, as in the case of amphotericin B constructs, enhanced, while CNTs are able to reduce the unwanted toxicity of the drug administered alone. Ammonium-functionalized CNTs can also be considered very promising vectors for gene-encoding nucleic acids. Indeed, we have formed stable complexes between cationic CNTs and plasmid DNA and demonstrated the enhancement of the gene therapeutic capacity in comparison to DNA alone. On the other hand, CNTs conjugated with antigenic peptides can be developed as a new and effective system for synthetic vaccine applications. What makes CNTs quite unique is their ability, first shown by our groups in 2004, to passively cross membranes of many different types of cells following a translocation mechanism that has been termed the nanoneedle mechanism. In that way, CNTs open innumerable possibilities for future drug discovery based on intracellular targets that have been hard to reach until today. Moreover, adequately functionalized CNTs as those shown in this Account can be rapidly eliminated from the body following systemic administration offering further encouragment for their development. CNT excretion rates and accumulation in organs and any reactivity with the immune system will determine the CNT safety profile and, consequently, any further pharmaceutical development. Caution is advised about the need for systematic data on the long-term fate of these very interesting and versatile nano-objects in correlation with the type of CNT material used. CNTs are gradually plyaing a bigger and more important role in the emerging field of nanomedicine; however, we need to guarantee that the great opportunities they offer will be translated into feasible and safe constructs to be included in drug discovery and development pipelines.

/pdf/functionalized-carbon-nanotubes-in-drug-design-and-discovery-3unuphb05b.pdf

Functionalized carbon nanotubes in drug design and discovery.

We report linear-response kinetic-energy density functionals, which show significant improvement over the Wang-Teter, Perrot, Smargiassi-Madden, Wang-Govind-Carter functionals, yet still maintain $\mathcal{O}(N\mathrm{ln}N)$ scaling. Numerical tests show that these functionals, which contain a double-density-dependent kernel, can reproduce the Kohn-Sham results almost exactly for several aluminum bulk phases. We further show that with a sensible choice of the uniform background density, energies of formation for the low-index aluminum surfaces, where the density variations are very large, can be reproduced to within reasonable accuracy.

/pdf/orbital-free-kinetic-energy-density-functionals-with-a-1hhoensh0q.pdf

Orbital-free kinetic-energy density functionals with a density-dependent kernel

In the beginning of quantum mechanical Density-Functional Theory (DFT), there was the Thomas-Fermi (TF) model, which uses the electron density p(r) (a function of only 3 coordinates) as the only physical variable. Calculations with this model were inexpensive but yielded poor numerical results due to a lack of understanding of exchange-correlation effects and the kinetic-energy density functional. Many years later, Hohenberg and Kohn (HK) established the formal foundation for DFT; Kohn and Sham (KS) devised a practical implementation and brought DFT into mainstream calculations of electronic structure. Although the KS formulation allows exact evaluation of the KS kinetic energy (Ts [p]), the one-electron orbitals introduced by the KS scheme inevitably encumber the formulation in three ways: (i) 3N (vs. 3) degrees of freedom, (ii) orbital orthonormalization, and (iii) Brillouin-zone (k-point) sampling in condensed phases. Given the accuracy of DFT with present exchange-correlation density functionals, it is logical to conclude that the last frontier in DFT is a better representation of the kinetic energy solely in terms of the density. If this is true, KS orbitals will be completely eliminated from DFT formulation, and the density can be solved directly from the TF-HK equation. This is certainly superior to the KS scheme because all energy terms can be computed in momentum space with an effectively linear scaling, O(MlnM), where M is the integration grid size. This work reviews major ideas in the design of such optimal orbital-free kinetic-energy density functionals and their applications.

Orbital-Free Kinetic-Energy Density Functional Theory

Chemistry of Single-Walled Carbon Nanotubes

The adsorption of small gaseous molecules to the metal center in Pt-doped (5,5) single-walled carbon nanotubes has been explored within density functional theory. A model system consisting of a single Pt atom residing in the middle of a carbon nanotube with capping H atoms is used for our investigation. For all gases studied, the overall process of adsorption was found to be exothermic, where the affinity strongly depended on the orientation of the molecule. By examining the density of states and molecular orbitals of these nanotube−adsorbate complexes in comparison to the bare Pt-doped nanotube, we show that the electronic structure of these materials is strongly influenced by the presence of gases. Hence, we propose an application of Pt-doped single-walled carbon nanotubes as gas sensors and hope to motivate experimental work in this field.

Adsorption of Small Gas Molecules onto Pt-Doped Single-Walled Carbon Nanotubes

The Staudinger reactions of substituted phosphanes and azides have been investigated by using density functional theory. Four different initial reaction mechanisms have been found. All systems studied go through a cis-transition state rather than a trans-transition state or a one-step transition state. The one-step pathway of the phosphorus atom attacking the substituted nitrogen atom is always unfavorable energetically. Depending on the substituents on the azide and the phosphane, the reaction mechanism with the lowest initial reaction barrier can be classified into three categories: (1). like the parent reaction, PH(3) + N(3)H, the reaction goes through a cis-transition state, approaches a cis-intermediate, overcomes a PN-bond-shifting transition state, reaches a four-membered ring intermediate, dissociates N(2) by overcoming a small barrier, and results in the final products: N(2) and a phosphazene; (2). once reaching the cis-intermediate, the reaction goes through the N(2)-eliminating transition state and produces the final products; (3). the reaction has a concerted initial cis-transition state, in which the phosphorus atom attacks the first and the third nitrogen atoms of the azide simultaneously and reaches an intermediate, and then the reaction goes through similar steps of the first reaction mechanism. In contrast to the previous predictions on the relative stability of the unsubstituted cis-configured phosphazide intermediate and the unsubstituted trans-configured phosphazide intermediate, the total energy of the substituted trans-configured phosphazide intermediate is close to that of the substituted cis-configured phosphazide intermediate. The preference of the initial cis-transition state reaction pathway is thoroughly discussed. The relative stability of the cis- and the trans-intermediates is explored and analyzed with the aid of molecular orbitals. The effects of substituents and solvent effects on the reaction mechanisms of the Staudinger reactions are discussed in detail.

Mechanisms of Staudinger reactions within density functional theory.

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