Modular Chemical Descriptor Language (MCDL): Stereochemical modules

<p>Abstract</p> <p>Background</p> <p>In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures.</p> <p>Results</p> <p>In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages.</p> <p>Conclusions</p> <p>Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.</p

A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)

A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI)

Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels

A new algorithm for divisive hierarchical clustering of chemical compounds based on 2D structural fragments is suggested. The algorithm is deterministic, and given a random ordering of the input, will always give the same clustering and can process a database up to 2 million records on a standard PC. The algorithm was used for classification of 1,183 antibiotics mixed with 999,994 random chemical structures. Similarity threshold, at which best separation of active and non active compounds took place, was estimated as 0.6. 85.7% of the antibiotics were successfully classified at this threshold with 0.4% of inaccurate compounds. A .sdf file was created with the probe molecules for clustering of external databases

Article Hierarchical Clustering of Large Databases and Classification of Antibiotics at High Noise Levels

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A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)

Abstract: A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI)

Determination of energy thresholds of electron excitations at semiconductor/insulator interfaces using trap-related displacement currents

Spectral measurements of illumination-induced displacement currents related to trapping of charge carriers optically excited in semiconductor electrodes are shown to deliver information regarding energy onsets of electron transitions at the interface. Presented examples include determination of the conduction band offset at the GaN/Al2O3 interface and determination of charge carrier excitation spectra of two-dimensional (2D) semiconductors MoS2 and WS2 at the interface with insulating SiO2

Band alignment at interfaces of two-dimensional materials: internal photoemission analysis

The article overviews experimental results obtained by applying internal photoemission (IPE) spectroscopy methods to characterize electron states in single- or few-monolayer thick two-dimensional materials and at their interfaces. Several conducting (graphene) and semiconducting (transitional metal dichalcogenides MoS2, WS2, MoSe2, and WSe2) films on top of thermal SiO2 have been analyzed by IPE, which reveals significant sensitivity of interface band offsets and barriers to the details of the material and interface fabrication, indicating violation of the Schottky-Mott rule. This variability is associated with charges and dipoles formed at the interfaces with van der Waals bonding as opposed to the chemically bonded interfaces of three-dimensional semiconductors and metals. Chemical modification of the underlying SiO2 surface is shown to be a significant factor, affecting interface barriers due to violation of the interface electroneutrality.status: publishe