Automated Identification and Classification of Stereochemistry: Chirality and Double Bond Stereoisomerism

Stereoisomers have the same molecular formula and the same atom connectivity and their existence can be related to the presence of different three-dimensional arrangements. Stereoisomerism is of great importance in many different fields since the molecular properties and biological effects of the stereoisomers are often significantly different. Most drugs for example, are often composed of a single stereoisomer of a compound, and while one of them may have therapeutic effects on the body, another may be toxic. A challenging task is the automatic detection of stereoisomers using line input specifications such as SMILES or InChI since it requires information about group theory (to distinguish stereoisomers using mathematical information about its symmetry), topology and geometry of the molecule. There are several software packages that include modules to handle stereochemistry, especially the ones to name a chemical structure and/or view, edit and generate chemical structure diagrams. However, there is a lack of software capable of automatically analyzing a molecule represented as a graph and generate a classification of the type of isomerism present in a given atom or bond. Considering the importance of stereoisomerism when comparing chemical structures, this report describes a computer program for analyzing and processing steric information contained in a chemical structure represented as a molecular graph and providing as output a binary classification of the isomer type based on the recommended conventions. Due to the complexity of the underlying issue, specification of stereochemical information is currently limited to explicit stereochemistry and to the two most common types of stereochemistry caused by asymmetry around carbon atoms: chiral atom and double bond. A Webtool to automatically identify and classify stereochemistry is available at http://nams.lasige.di.fc.ul.pt/tools.ph

Colossal infrared and terahertz magneto-optical activity in a two-dimensional Dirac material

When two-dimensional electron gases (2DEGs) are exposed to magnetic field, they resonantly absorb electromagnetic radiation via electronic transitions between Landau levels (LLs). In 2DEGs with a Dirac spectrum, such as graphene, theory predicts an exceptionally high infrared magneto-absorption, even at zero doping. However, the measured LL magneto-optical effects in graphene have been much weaker than expected because of imperfections in the samples available so far for such experiments. Here we measure magneto-transmission and Faraday rotation in high-mobility encapsulated monolayer graphene using a custom designed setup for magneto-infrared microspectroscopy. Our results show a strongly enhanced magneto-optical activity in the infrared and terahertz ranges characterized by a maximum allowed (50%) absorption of light, a 100% magnetic circular dichroism as well as a record high Faraday rotation. Considering that sizeable effects have been already observed at routinely achievable magnetic fields, our findings demonstrate a new potential of magnetic tuning in 2D Dirac materials for long-wavelength optoelectronics and plasmonics.Comment: 14 pages, 4 figure

H\"older mean applied to Anderson localization

The phase diagram of correlated, disordered electron systems is calculated within dynamical mean-field theory using the H\"older mean local density of states. A critical disorder strength is determined in the Anderson-Falicov-Kimball model and the arithmetically and the geometrically averages are found to be just particular means used respectively to detect or not the Anderson localization. Correlated metal, Mott insulator and Anderson insulator phases, as well as coexistence and crossover regimes are analyzed in this new perspective.Comment: 6 pages, 6 figures: Phys. Rev. B 76, 035111 (2007

Dynamical matrix for arbitrary quadratic fermionic bath Hamiltonians and non-Markovian dynamics of one and two qubits in an Ising model environment

We obtain the analytical expression for the Kraus decomposition of the quantum map of an environment modeled by an arbitrary quadratic fermionic Hamiltonian acting on one or two qubits, and derive simple functions to check the non-positivity of the intermediate map. These functions correspond to two different sufficient criteria for non-Markovianity. In the particular case of an environment represented by the Ising Hamiltonian, we discuss the two sources of non-Markovianity in the model, one due to the finite size of the lattice, and another due to the kind of interactions.Comment: 11 pages, 10 figure

Patents and Competition in the Automobile Industry

Methane (CH4) fluxes from world rivers are still poorly constrained, with measurements restricted mainly to temperate climates. Additional river flux measurements, including spatio-temporal studies, are important to refine extrapolations. Here we assess the spatio-temporal variability of CH4 fluxes from the Amazon and its main tributaries, the Negro, Solimoes, Madeira, Tapajos, Xingu, and Para Rivers, based on direct measurements using floating chambers. Sixteen of 34 sites were measured during low and high water seasons. Significant differences were observed within sites in the same river and among different rivers, types of rivers, and seasons. Ebullition contributed to more than 50% of total emissions for some rivers. Considering only river channels, our data indicate that large rivers in the Amazon Basin release between 0.40 and 0.58 Tg CH4 yr(-1). Thus, our estimates of CH4 flux from all tropical rivers and rivers globally were, respectively, 19-51% to 31-84% higher than previous estimates, with large rivers of the Amazon accounting for 22-28% of global river CH4 emissions.Funding Agencies|FAPESP [08/58089-9, 2011/06609-1, 2011/14502-2, 2012/17359-9]</p

Exchange-correlation functionals from the strongly-interacting limit of DFT: Applications to model chemical systems

We study model one-dimensional chemical systems (representative of their three-dimensional counterparts) using the strictly-correlated electrons (SCE) functional, which, by construction, becomes asymptotically exact in the limit of infinite coupling strength. The SCE functional has a highly non-local dependence on the density and is able to capture strong correlation within Kohn- Sham theory without introducing any symmetry breaking. Chemical systems, however, are not close enough to the strong-interaction limit so that, while ionization energies and the stretched H2 molecule are accurately described, total energies are in general way too low. A correction based on the exact next leading order in the expansion at infinite coupling strength of the Hohenberg-Kohn functional largely improves the results.Comment: 9 pages, 6 figures. Submitted to PCCP's Themed Collection on Density Functional Theory and its Application

Geotechnical Evaluation of Road Failure along 20th Street BDPA, Benin City, Nigeria

This work investigated the cause of road failure using geotechnical analysis along the 20th Street, BDPA, Benin-city, Nigeria. Soil samples from the failed section of the road were analyzed to ascertain their particle size distribution, limit liquid, plastic limit, maximum dry density, optimum moisture content and California bearing ratio using the British Standard Institution (BS 1377 1990). The result from the particle size distribution analysis showed that soils were well graded (GW) with percentage fines ranging from 26 to 49.7%, specific gravity from 2.4 to 2.6, liquid limit from 21.52-29.79%, plastic limit ranged from 11.73-18.80%, plasticity index 8.29-12.49% and California bearing ratio(unsoaked) from 9-29%. The compaction test results showed that the Maximum Dry Density (MDD) ranged from 1.7mg/m3-1.8mg/m3 and Optimum Maximum Content from 11-14%. It was found that there is a significant difference between the geotechnical characteristics of the soil and the standard for geotechnical characteristics set by the Federal Ministry of Works. This led to the conclusion that the soil geotechnical characteristics is a causative factor of road failure as well as the geology. Hence, it was recommended that the geotechnical and geological characteristics of sub-grades and fill materials be taken into consideration during road construction