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Papers by Markus Meringer

Astrobiology, 2015

Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a ce... more Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored. Key Words: Evolution-Chemical evolution-Exobiology-Prebiotic chemistry-RNA world. Astrobiology 15, 538-558.

Chemoinformatics is the interdisciplinary scientific field that develops computational methods fo... more Chemoinformatics is the interdisciplinary scientific field that develops computational methods for processing chemical data. Structure generation techniques offer unique ways to systematically create molecules ‘in silico’ that are not (yet) present in any database. This talk will give a survey of the most important ideas and methods underlying such structure generation algorithms. Starting from a brief historical overview, including typical applications of structure generators, I will conclude with an outline of current projects and plans that might pave the way towards a better understanding of the biochemical foundations of life's origins.

In den letzten Jahren sind in der Chemie ganz neue Methoden der Massensynthese 1 entwickelt worde... more In den letzten Jahren sind in der Chemie ganz neue Methoden der Massensynthese 1 entwickelt worden, die mittlerweile ins Zentrum des Interesses und der Diskussion gerückt sind. Sie werden u.a. im pharmazeutischen Bereich und in den Materialwissenschaften angewendet und unter der Überschrift kombinatorische Chemie zusammengefaßt. Es geht dabei um die durch Roboter unterstützte und gesteuerte Erzeugung von Hunderten oder gar Tausenden chemischer Substanzen "auf einen Schlag". Schon der Name kombinatorische Chemie läßt Mathematiker und Informatiker aufhorchen. Er zeigt deutlich, daß begleitende mathematisch-kombinatorische Überlegungen im Vorfeld solcher Experimente von Nutzen sein sollten. Da es sich dabei um Massensynthese handelt, sieht der Informatiker sofort, daß bei Experimenten der kombinatorischen Chemie eine riesige Datenflut anfallen wird, die es zu strukturieren gilt. Wir wollen deshalb hier unsere Erfahrungen schildern, die wir im Rahmen zweier Projekte gemacht haben, und wir werden einige der Probleme aufzeigen, die wir in diesem Zusammenhang lösen wollen. Es handelt sich dabei um ein DFG-Projekt zur Materialforschung (gemeinsam mit Prof. Ziegler, FAN) von Precursorkeramiken, und ein BMBF-Projekt (Federführung Fa. Henkel) zur Optimierung und Analyse solcher Verfahren.

After a few remarks on the history of molecular modelling we de- scribe certain mathematical aspe... more After a few remarks on the history of molecular modelling we de- scribe certain mathematical aspects of the generation of molecular structural formulae. The focus is on the automatic generation of struc- tural formulae for the purpose of molecular structure elucidation and the examination of molecular libraries. The aim is to give a review and to point to relevant literature.

The generation of molecular graphs by computer programs has undergone some changes. The developme... more The generation of molecular graphs by computer programs has undergone some changes. The development is reported with focus on various mathematical methods that are created and employed in this process. No attempt has been made to explicitely state and prove the theorems but this overview contains hints to the relevant literature. In particular, a new generator MOLGEN 4.0 is described

Abstract: IntroductionMost of the computer programs used for automatic spectra interpretation dep... more Abstract: IntroductionMost of the computer programs used for automatic spectra interpretation dependon large spectral databases. 1 The experimental spectrum in question is comparedwith the entries of the database and the structures of the most similar spectra aregiven as possible solutions. This method has several limitations: (a) The quality ofthe database spectra restricts the performance; even good experimental spectra maylead to

DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 2000

The generation of discrete structures up to isomorphism is interesting as well for theoretical as... more The generation of discrete structures up to isomorphism is interesting as well for theoretical as for practical purposes. Mathematicians want to look at and analyse structures and for example chemical industry uses mathematical generators of isomers for structure elucidation. The example chosen in this paper for explaining general generation methods is a relatively far reaching and fast graph generator which

Scientific Computing in Chemical Engineering II, 1999

ABSTRACT Some of the mathematical methods will be described which are implemented in the software... more ABSTRACT Some of the mathematical methods will be described which are implemented in the software package MOLCOMB 1 that allows to simulate combinatorial chemistry by generating combinatorial libraries and to do screening according to geometric substructures. 1 Combinatorial Chemistry To begin with, we consider the examples described in the prominent papers [1] and [2] on combinatorial chemistry. The authors introduce particular combinatorial libraries obtained by starting from the central molecules Cl Cl Cl Cl O O O O O Cl Cl Cl Cl O O O O Cl Cl O Cl O O i.e. they start from cubane, xanthene, benzene triacid chlorine as central molecules to which they attach amino acids according to the reaction scheme that describes the reaction between the active sites 1 MOLCOMB is the outcome of a research project supported by the federal ministery for technology, under contract 03 KE7BA 1-4 C 3 2 1 Cl O of the central molecule and the active parts of the aminoacids in question: C O 1 2 3 4 5 C...

Advances in Mathematical Chemistry and Applications, 2014

Page 1. Erzeugung regulärer Graphen Markus Meringer + + + + + Bayreuth, Januar 1996 Diplomarbeit ... more Page 1. Erzeugung regulärer Graphen Markus Meringer + + + + + Bayreuth, Januar 1996 Diplomarbeit bei Prof. Dr. Laue Lehrstuhl II für Mathematik der Universität Bayreuth Page 2. ii Page 3. iii Vorwort ...

Scientific Reports, 2015

Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically en... more Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or ''chemistry space.'' Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.

In information processing, in combinatorial chemistry, in structure elucidation, and in several o... more In information processing, in combinatorial chemistry, in structure elucidation, and in several other fields of chemistry, the computer-aided generation of all structures (constitutional formulae) within a defined structure space has become increasingly important. In this brief review the mathematical foundations of the classical molecular model and thus of the generation process are outlined, and the current state of structure generation as applied in software developed by the Bayreuth group is discussed.

SCIAMACHY on ENVISAT has meanwhile explored the Earth's atmosphere for more than 9 years. All sub... more SCIAMACHY on ENVISAT has meanwhile explored the Earth's atmosphere for more than 9 years. All subsystems perform well which is a precondition for maintaining a high optical and operational performance. Even the unavoidable in-orbit degradation due to the harsh space environment is lower than expected and can be largely compensated by sophisticated calibration and monitoring means. Because of the excellent status of both the platform and the instruments the ENVISAT mission has been extended until the end of 2013. Associated with this extension was a change of the orbit in late October 2010 and reconfiguring SCIAMACHY for achieving successful operations in the coming years.

Astrobiology, 2015

Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a ce... more Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored. Key Words: Evolution-Chemical evolution-Exobiology-Prebiotic chemistry-RNA world. Astrobiology 15, 538-558.

Chemoinformatics is the interdisciplinary scientific field that develops computational methods fo... more Chemoinformatics is the interdisciplinary scientific field that develops computational methods for processing chemical data. Structure generation techniques offer unique ways to systematically create molecules ‘in silico’ that are not (yet) present in any database. This talk will give a survey of the most important ideas and methods underlying such structure generation algorithms. Starting from a brief historical overview, including typical applications of structure generators, I will conclude with an outline of current projects and plans that might pave the way towards a better understanding of the biochemical foundations of life's origins.

In den letzten Jahren sind in der Chemie ganz neue Methoden der Massensynthese 1 entwickelt worde... more In den letzten Jahren sind in der Chemie ganz neue Methoden der Massensynthese 1 entwickelt worden, die mittlerweile ins Zentrum des Interesses und der Diskussion gerückt sind. Sie werden u.a. im pharmazeutischen Bereich und in den Materialwissenschaften angewendet und unter der Überschrift kombinatorische Chemie zusammengefaßt. Es geht dabei um die durch Roboter unterstützte und gesteuerte Erzeugung von Hunderten oder gar Tausenden chemischer Substanzen "auf einen Schlag". Schon der Name kombinatorische Chemie läßt Mathematiker und Informatiker aufhorchen. Er zeigt deutlich, daß begleitende mathematisch-kombinatorische Überlegungen im Vorfeld solcher Experimente von Nutzen sein sollten. Da es sich dabei um Massensynthese handelt, sieht der Informatiker sofort, daß bei Experimenten der kombinatorischen Chemie eine riesige Datenflut anfallen wird, die es zu strukturieren gilt. Wir wollen deshalb hier unsere Erfahrungen schildern, die wir im Rahmen zweier Projekte gemacht haben, und wir werden einige der Probleme aufzeigen, die wir in diesem Zusammenhang lösen wollen. Es handelt sich dabei um ein DFG-Projekt zur Materialforschung (gemeinsam mit Prof. Ziegler, FAN) von Precursorkeramiken, und ein BMBF-Projekt (Federführung Fa. Henkel) zur Optimierung und Analyse solcher Verfahren.

After a few remarks on the history of molecular modelling we de- scribe certain mathematical aspe... more After a few remarks on the history of molecular modelling we de- scribe certain mathematical aspects of the generation of molecular structural formulae. The focus is on the automatic generation of struc- tural formulae for the purpose of molecular structure elucidation and the examination of molecular libraries. The aim is to give a review and to point to relevant literature.

The generation of molecular graphs by computer programs has undergone some changes. The developme... more The generation of molecular graphs by computer programs has undergone some changes. The development is reported with focus on various mathematical methods that are created and employed in this process. No attempt has been made to explicitely state and prove the theorems but this overview contains hints to the relevant literature. In particular, a new generator MOLGEN 4.0 is described

Abstract: IntroductionMost of the computer programs used for automatic spectra interpretation dep... more Abstract: IntroductionMost of the computer programs used for automatic spectra interpretation dependon large spectral databases. 1 The experimental spectrum in question is comparedwith the entries of the database and the structures of the most similar spectra aregiven as possible solutions. This method has several limitations: (a) The quality ofthe database spectra restricts the performance; even good experimental spectra maylead to

DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 2000

The generation of discrete structures up to isomorphism is interesting as well for theoretical as... more The generation of discrete structures up to isomorphism is interesting as well for theoretical as for practical purposes. Mathematicians want to look at and analyse structures and for example chemical industry uses mathematical generators of isomers for structure elucidation. The example chosen in this paper for explaining general generation methods is a relatively far reaching and fast graph generator which

Scientific Computing in Chemical Engineering II, 1999

ABSTRACT Some of the mathematical methods will be described which are implemented in the software... more ABSTRACT Some of the mathematical methods will be described which are implemented in the software package MOLCOMB 1 that allows to simulate combinatorial chemistry by generating combinatorial libraries and to do screening according to geometric substructures. 1 Combinatorial Chemistry To begin with, we consider the examples described in the prominent papers [1] and [2] on combinatorial chemistry. The authors introduce particular combinatorial libraries obtained by starting from the central molecules Cl Cl Cl Cl O O O O O Cl Cl Cl Cl O O O O Cl Cl O Cl O O i.e. they start from cubane, xanthene, benzene triacid chlorine as central molecules to which they attach amino acids according to the reaction scheme that describes the reaction between the active sites 1 MOLCOMB is the outcome of a research project supported by the federal ministery for technology, under contract 03 KE7BA 1-4 C 3 2 1 Cl O of the central molecule and the active parts of the aminoacids in question: C O 1 2 3 4 5 C...

Advances in Mathematical Chemistry and Applications, 2014

Page 1. Erzeugung regulärer Graphen Markus Meringer + + + + + Bayreuth, Januar 1996 Diplomarbeit ... more Page 1. Erzeugung regulärer Graphen Markus Meringer + + + + + Bayreuth, Januar 1996 Diplomarbeit bei Prof. Dr. Laue Lehrstuhl II für Mathematik der Universität Bayreuth Page 2. ii Page 3. iii Vorwort ...

Scientific Reports, 2015

Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically en... more Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or ''chemistry space.'' Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.

In information processing, in combinatorial chemistry, in structure elucidation, and in several o... more In information processing, in combinatorial chemistry, in structure elucidation, and in several other fields of chemistry, the computer-aided generation of all structures (constitutional formulae) within a defined structure space has become increasingly important. In this brief review the mathematical foundations of the classical molecular model and thus of the generation process are outlined, and the current state of structure generation as applied in software developed by the Bayreuth group is discussed.

SCIAMACHY on ENVISAT has meanwhile explored the Earth's atmosphere for more than 9 years. All sub... more SCIAMACHY on ENVISAT has meanwhile explored the Earth's atmosphere for more than 9 years. All subsystems perform well which is a precondition for maintaining a high optical and operational performance. Even the unavoidable in-orbit degradation due to the harsh space environment is lower than expected and can be largely compensated by sophisticated calibration and monitoring means. Because of the excellent status of both the platform and the instruments the ENVISAT mission has been extended until the end of 2013. Associated with this extension was a change of the orbit in late October 2010 and reconfiguring SCIAMACHY for achieving successful operations in the coming years.