Axel Drefahl

Publications

• CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures.

  Axel Drefahl

  Journal of cheminformatics. 01/2011; 3(1):1.

  CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at ... [more] CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity.

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• Quantitative Property-Property Relationships (QPPRs) and Molecular-Similarity Methods for Estimating Flash Points of Si-Organic and Ge-Organic Compounds

  Axel Drefahl

  iEMSs Third Biennial Meeting, "Summit on Environmental Modelling and Software"; 01/2006

  Good correlations between normal boiling points and flash points of Si-organic and Ge-organic compounds have been found. These correlations are discussed and compared with known boiling-point/flash-point correlations of organic compounds. Since boiling point data are often not available, application... [more] Good correlations between normal boiling points and flash points of Si-organic and Ge-organic compounds have been found. These correlations are discussed and compared with known boiling-point/flash-point correlations of organic compounds. Since boiling point data are often not available, application of molecular-similarity methods for the estimation of flash points of query compounds from flash points of structurally related source compounds in a database have been explored. Relationships, called quantitative source-target differences (QSTDs), that allow the estimation of a query (new target) from database compounds (source compounds) have been developed. For example, the QSTD relationship, Tf{R4Ge}/ºC = 19.0474 + 0.9149 ·Tf{R4Si}/ºC (m = 13, r = 0.9832), allows the estimation of the flash point (Tf) of a Ge-organic compound from the known flash point of the analogous compound that contains a Si atom instead of a Ge atom, but otherwise has the same molecular structure as the query. Further, QSTDs to estimate flash points of Si-organic compounds from related Si-organic compounds are presented. The QSTD approach additionally allows to predict lower and upper boundary values between which the true flash point of a query compound will be found with high probability. Applications of this approach with respect to flammability classification and fire hazard assessment are discussed.

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• Handbook for Estimating Physicochemical Properties of Organic Compounds

  Axel Drefahl, Martin Reinhard

  07/1999: pages 1-228;

  ISBN: 0-471-17264-2

• Similarity-based search and evaluation of environmentally relevant properties for organic compounds in combination with the group contribution approach

  Axel Drefahl, Martin Reinhard

  J. Chem. Inf. Comput. Sci. 01/1993; 33:886-895.

  A novel knowledge-based data evaluation system for organic compounds, DESOC, has been developed. DESOC comprises a compound/property database and several modules for the prediction of properties. The database contains compounds that are represented by SMILES notations. Property data are Antoine coef... [more] A novel knowledge-based data evaluation system for organic compounds, DESOC, has been developed. DESOC comprises a compound/property database and several modules for the prediction of properties. The database contains compounds that are represented by SMILES notations. Property data are Antoine coefficients for temperature-dependent vapor pressure calculations, aqueous solubility data at 20 and 25 ºC, and partition coefficients for the system air/water, 1-octanol/water, and soil/water. DESOC includes routines for data retrieval, similarity-based search, and property estimation. Estimation of a query property is based on (1) identification of database compounds structurally related to the query, (2) recognition of the structural difference between query and database compounds, and (3) translation of the structural difference into the corresponding property difference. A new approach, the group interchange method (GIM), is introduced for the representation and analysis of structural differences between similar compounds. Compounds are related to each other in terms of elementary group operations. These operations are encoded as linear notations using the grammar of SMILES. The performance of DESOC is illustrated by protocol files generated for selected queries.

• Modeling of organic compounds to predict their environmental fate based on substructure and physicochemical parameters

  Axel Drefahl

  01/1988

  Degree: Ph. D. (Chemistry)

  Supervisor: Prof. Ivar Ugi