Literature about MOLGEN

Structure generation

  • C. Rücker, M. Meringer, A. Wassermann: Comment on “Nomenclature, Chemical Abstracts Service Numbers, Isomer Enumeration, Ring Strain, and Stereochemistry: What Does Any of This Have to Do with an International Chemical Disarmament and Nonproliferation Treaty?”. Journal of Chemical Education, 2021, https://pubs.acs.org/doi/10.1021/acs.jchemed.1c00134.
  • H. J. Cleaves, C. Butch, P. B. Burger, J. Goodwin, M. Meringer: One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules. J. Chem. Inf. Model. 59, 4266-4277, 2019.
  • M. Meringer, H. J. Cleaves: Exploring astrobiology using in silico molecular structure generation. Phil. Trans. R. Soc. A 375, 2017. (pdf)
  • R. Gugisch, A. Kerber, A. Kohnert, R. Laue, M. Meringer, C. Rücker, A. Wassermann: MOLGEN 5.0, a Molecular Structure Generator. In S.C. Basak, G. Restrepo, J. L. Villaveces, eds, Advances in Mathematical Chemistry and Applications, volume 1, pages 113–138. Bentham, Sharjah, UAE, 2014. (pdf)
  • M. Meringer, H. J. Cleaves, S. J. Freeland: Beyond Terrestrial Biology: Charting the Chemical Universe of α-Amino Acid Structures. J. Chem. Inf. Model. 53, 2851-2862, 2013.
  • M. Meringer: Structure Enumeration and Sampling. Handbook of Chemoinformatics Algorithms, CRC/Chapman&Hall, 233-267, 2010. (pdf)
  • R. Gugisch, C. Rücker: Unified Generation of Conformations, Conformers, and Stereoisomers: A Discrete Mathematics-Based Approach. MATCH Commun. Math. Comput. Chem. 61, 117-148, 2009.
  • A. Kerber, R. Laue, M. Meringer, C. Rücker: Molecules in Silico: A Graph Description of Chemical Reactions. J. Chem. Inf. Model. 47, 805-817, 2007. (pdf)
  • R. Laue, T. Grüner, M. Meringer, A. Kerber: Constrained Generation of Molecular Graphs. DIMACS Series in Discrete Mathematics And Theoretical Computer Science 69, 319-332, 2005 (pdf)
  • C. Rücker, R. Gugisch, A. Kerber: Manual Construction and Mathematics- and Computer-Aided Counting of Stereoisomers. The Example of Inositols. J. Chem. Inf. Comput. Sci. 44, 1654-1665, 2004.
  • J. Braun, R. Gugisch, A. Kerber, R. Laue, M. Meringer, C. Rücker: MOLGEN-CID - A Canonizer for Molecules and Graphs Accessible through the Internet. J. Chem. Inf. Comput. Sci. 44, 542-548, 2004. (pdf)
  • R. Gugisch, A. Kerber, R. Laue, M. Meringer, C. Rücker: Kombinatorische Chemie, eine Herausforderung für Mathematik und Informatik. Spektrum 1/02, Universität Bayreuth, 64-67, 2002. (pdf)
  • R. Gugisch, A. Kerber, R. Laue, M. Meringer, J. Weidinger: MOLGEN-COMB, a Software Package for Combinatorial Chemistry. MATCH Commun. Math. Comput. Chem. 41, 189-203, 2000. (pdf)
  • T. Grüner, A. Kerber, R. Laue, M. Meringer: Mathematics for Combinatorial Chemistry. Scientific Computing in Chemical Engineering II, 74-81, Springer-Verlag 1999. (pdf)
  • A. Kerber, R. Laue, T. Grüner, M. Meringer: MOLGEN 4.0. MATCH Commun. Math. Comput. Chem. 37, 205-208, 1998. (pdf)
  • A. Kerber, R. Laue, T. Wieland: Erkennung, Beschreibung und Visualisierung molekularer Strukturen, Proceedings of the BMBF Statusseminar Application-oriented joint projects in the field of mathematics.
  • T. Wieland, A. Kerber, R. Laue: Principles of the generation of constitutional and configurational isomers, J. Chem. Inf. Comput. Sci. 36, 413-419, 1996.
  • C. Benecke, R. Grund, R. Hohberger, A. Kerber, R. Laue, T. Wieland: MOLGEN+, a generator of connectivity isomers and stereoisomers for molecular structure elucidation , Anal. Chim. Acta 314, 141-147, 1995.
  • T. Wieland: Erzeugung, Abzählung und Konstruktion von Stereoisomeren, MATCH Commun. Math. Comput. Chem. 31, 153-203, 1994.
  • T. Wieland: Computerunterstützte Berechnung von Stereoisomeren. Master's thesis, University of Bayreuth, 1994.

Structure elucidation

  • S. Devata, H. J. Cleaves, J. Dimandja, C. A. Heist, M. Meringer: Comparative evaluation of electron ionization mass spectral prediction methods. Journal of the American Society for Mass Spectrometry 34 (8), 1584-1592, 2023.
  • M. Meringer, C. Giri, H. J. Cleaves: Fitting Cometary Sampling and Composition Mass Spectral Results Using Non-negative Least Squares: Reducing Detection Ambiguity for In Situ Solar System Organic Compound Measurements. ACS Earth and Space Chemistry 2, 1256-1261, 2018.
  • M. Meringer, E. L. Schymanski: Small Molecule Identification with MOLGEN and Mass Spectrometry. Metabolites 3, 440-462, 2013. (pdf)
  • E. L. Schymanski, C. M. J. Gallampois, M. Krauss, M. Meringer, S. Neumann, T. Schulze, S. Wolf, W. Brack: Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties. Anal. Chem. 84, 3287-3295, 2012.
  • M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. (pdf)
  • E. L. Schymanski, M. Meringer, W. Brack: Automated Strategies To Identify Compounds on the Basis of GC/EI-MS and Calculated Properties. Anal. Chem. 83, 903-912, 2011.
  • E. L. Schymanski, M. Meringer, W. Brack : Matching Structures to Mass Spectra Using Fragmentation Patterns - Are the Results as Good as they Look? Analytical Chemistry 81, 3608-17, 2009.
  • E. L. Schymanski, C. Meinert, M. Meringer, W. Brack : The Use of MS Classifiers and Structure Generation to Assist in the Identification of Unknowns in Effect-Directed Analysis. Analytica Chimica Acta 615 (2), 136-147, 2008.
  • A. Kerber, M. Meringer, C. Rücker: CASE via MS: Ranking Structure Candidates by Mass Spectra. Croatica Chemica Acta 79, 449-464, 2006. (pdf)
  • J. Meiler, M. Meringer: Ranking MOLGEN Structure Proposals by 13C NMR Chemical Shift Prediction with ANALYZE. MATCH Commun. Math. Comput. Chem. 45, 85-108, 2002. (pdf)
  • A. Kerber, R. Laue, M. Meringer and K. Varmuza: MOLGEN-MS: Evaluation of Low Resolution Electron Impact Mass Spectra with MS Classification and Exhaustive Structure Generation. Advances in Mass Spectrometry 15, 939-940, Wiley 2001. (pdf)
  • T. Grüner, A. Kerber, R. Laue, M. Liepelt, M. Meringer, K. Varmuza, W. Werther: Bestimmung von Summenformeln aus Massenspektren durch Erkennung überlagerter Isotopenmuster. MATCH Commun. Math. Comput. Chem. 37, 163-177, 1998. (pdf)

QSAR/QSPR

  • C. Rücker, G. Rücker, M. Meringer: y-Randomization and Its Variants in QSPR/QSAR. J. Chem. Inf. Model. 47, 2345-2357, 2007. (pdf)
  • C. Rücker, M. Scarsi, M. Meringer: QSAR of PPARγ Agonist Binding and Transactivation . Bioorg. Med. Chem. 14, 5178-5195, 2006. (pdf)
  • C. Rücker, M. Meringer, A. Kerber: QSPR Using MOLGEN-QSPR: The Challenge of Fluoroalkane Boiling Points. J. Chem. Inf. Model. 45, 74-80, 2005. (pdf)
  • J. Braun, A. Kerber, M. Meringer, C. Rücker: Similarity of Molecular Descriptors: The Equivalence of Zagreb Indices and Walk Counts. MATCH Commun. Math. Comput. Chem. 54, 163-176, 2005. (pdf)
  • C. Rücker, M. Meringer, A. Kerber: QSPR Using MOLGEN-QSPR: The Example of Haloalkane Boiling Points. J. Chem. Inf. Comput. Sci. 44, 2070-2076, 2004. (pdf)
  • A. Kerber, R. Laue, M. Meringer, C. Rücker: MOLGEN-QSPR, a Software Package for the Study of Quantitative Structure Property Relationships. MATCH Commun. Math. Comput. Chem. 51, 187-204, 2004. (pdf)

Mixed and miscellaneous

  • C. Rücker, D. Troegel, K. Kümmerer: Atmospheric oxidation of dimethylsiloxanes, a source of Si=O double bonds? Environmental Science and Pollution Research , 32, 26611-26628, 2025. https://doi.org/10.1007/s11356-025-37108-6.
  • M. Meringer, G. M. Casanola-Martin, B. Rasulev, H. J. Cleaves: Similarity Analysis of Computer-Generated and Commercial Libraries for Targeted Biocompatible Coded Amino Acid Replacement. International Journal of Molecular Sciences 25 (22), 12343, 2024. (pdf)
  • R. Yi, T. Z. Jia, M. Meringer, L. K. Marshall, C. Chen, S. E. McGlynn, A. C. Fahrenbach, H. J. Cleaves: Alternating co-synthesis of glycol nucleic acid (GNA) monomers with dicarboxylic acids via drying. Chemical Communications 59 (45), 6865-6868, 2023.
  • M. Ilardo, R. Bose, M. Meringer, B. Rasulev, N. Grefenstette, J. Stephenson, S. Freeland, R. J. Gillams, C. J Butch, H. J. Cleaves: Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets. Scientific Reports 9, 2019. (pdf)
  • M. Meringer, H. J. Cleaves: Computational exploration of the chemical structure space of possible reverse tricarboxylic acid cycle constituents. Scientific Reports 7, 2017. (pdf)
  • H. J. Cleaves, M. Meringer, J. Goodwin: 227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space? Astrobiology 15 (7), 538-558, 2015.
  • M. Ilardo, M. Meringer, S. J. Freeland, B. Rasulev, H. J. Cleaves: Extraordinarily adaptive properties of the genetically encoded amino acids. Scientific Reports 5, 2015.
  • A. Kerber, R.Laue, M. Meringer, C. Rücker, E. Schymanski: Mathematical Chemistry and Chemoinformatics. Structure Generation, Elucidation and Quantitative Structure-Property Relationships. De Gruyter, 520 pages, 2013.
  • R. Gugisch, A. Kerber, R.Laue, M. Meringer, C. Rücker: History and Progress of the Generation of Structural Formulae in Chemistry and its Applications. MATCH Commun. Math. Comput. Chem. 58, 239-280, 2007. (pdf)
  • A. Kerber, R. Laue, M. Meringer, C. Rücker: Molecules in Silico: Potential versus Known Organic Compounds. MATCH Commun. Math. Comput. Chem. 54, 301-312, 2005. (pdf)
  • A. Kerber, R. Laue, M. Meringer, C. Rücker: Molecules in Silico: The Generation of Structural Formulae and Its Applications. J. Comput. Chem. Jpn 3, 85-96, 2004. (pdf)
  • M. Meringer: Mathematische Modelle für die kombinatorische Chemie und die molekulare Strukturaufklärung. Doctoral thesis, Universität Bayreuth, May 2004. Published by Logos-Verlag, Berlin. (354 pages; Also available: Kurzfassung/ Abstract).
  • A. Kerber, R. Laue, M. Meringer: An application of the structure generator MOLGEN to patents in chemistry. MATCH Commun. Math. Comput. Chem. 47, 169-172, 2003. (pdf)
  • C. Rücker, J. Braun: UNIMOLIS - A computer-aided course on molecular symmetry and isomerism. MATCH Commun. Math. Comput. Chem. 47, 173-174, 2003.
  • C. Rücker, G. Rücker, M. Meringer: Exploring the Limits of Graph Invariant- and Spectrum-Based Discrimination of (Sub)structures. J. Chem. Inf. Comput. Sci. 42, 640-650, 2002. (pdf)
  • C. Rücker, M. Meringer: How Many Organic Compounds are Graph-Theoretically Nonplanar? MATCH Commun. Math. Comput. Chem. 45, 153-172, 2002. (pdf)
  • G. Brinkmann, M. Meringer: The smallest 4-regular 4-chromatic graphs with girth 5. Graph Theory Notes of New York 32, 40-41, 1997 (pdf)
  • T. Wieland: Mathematical Simulations in Combinatorial Chemistry, MATCH Commun. Math. Comput. Chem. 34, 179-206, 1996.
  • T. Grüner, R. Laue, M. Meringer: Algorithms for group actions: homomorphism principle and orderly generation applied to graphs. In DIMACS series in discrete Mathematics and theoretical computer science, American Mathematical Society, 113-122, 1996 (pdf)
  • M. Meringer: Erzeugung regulärer Graphen Diplomarbeit, Universität Bayreuth, 1996 (pdf)
  • C. Benecke, R. Grund, A. Kerber, R. Laue, T. Wieland: Chemical Education via MOLGEN, J. Chem. Educ. 72, 403-406, 1995.

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