33,538 research outputs found
Benchmarking the SPARC software program for estimating solubilities of naphthalene and anthracene in organic solvents
The SPARC software program was benchmarked for calculating the solubilities of two representative polyaromatic hydrocarbons (PAHs), naphthalene and anthracene, in a range of organic solvents at various temperatures. Although SPARC was able to reasonably approximate the solubilities of naphthalene in some organic solvents, gross errors were obtained for other solvents. For anthracene, poor prediction performance was observed in all solvents considered. Overall, the results suggest that SPARC is currently not suitable for accurately predicting the solubilities of representative PAHs relevant for the petroleum sector in various organic solvents
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
Machine Learning, Quantum Mechanics, and Chemical Compound Space
We review recent studies dealing with the generation of machine learning
models of molecular and solid properties. The models are trained and validated
using standard quantum chemistry results obtained for organic molecules and
materials selected from chemical space at random
Extended Huckel theory for bandstructure, chemistry, and transport. II. Silicon
In this second paper, we develop transferable semi-empirical parameters for
the technologically important material, silicon, using Extended Huckel Theory
(EHT) to calculate its electronic structure. The EHT-parameters areoptimized to
experimental target values of the band dispersion of bulk-silicon. We obtain a
very good quantitative match to the bandstructure characteristics such as
bandedges and effective masses, which are competitive with the values obtained
within an orthogonal-tight binding model for silicon. The
transferability of the parameters is investigated applying them to different
physical and chemical environments by calculating the bandstructure of two
reconstructed surfaces with different orientations: Si(100) (2x1) and Si(111)
(2x1). The reproduced - and -surface bands agree in part
quantitatively with DFT-GW calculations and PES/IPES experiments demonstrating
their robustness to environmental changes. We further apply the silicon
parameters to describe the 1D band dispersion of a unrelaxed rectangular
silicon nanowire (SiNW) and demonstrate the EHT-approach of surface passivation
using hydrogen. Our EHT-parameters thus provide a quantitative model of
bulk-silicon and silicon-based materials such as contacts and surfaces, which
are essential ingredients towards a quantitative quantum transport simulation
through silicon-based heterostructures.Comment: 9 pages, 9 figure
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