Accurate Analysis of Formose Reaction Products by LC–UV: An Analytical Challenge

Zweckmair, Thomas; Böhmdorfer, Stefan; Bogolitsyna, Anna; Rosenau, Thomas; Potthast, Antje; Novalin, Senad

doi:10.1093/chromsci/bmt004

Cited by 18 publications

(27 citation statements)

References 17 publications

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“…These,h owever,a re higher in score than the best PQ option (35), so the algorithm reverts "locally" into node 8, finds nothing to explore there,r everts into node 5 (better than 35 in the PQ) and expands into node with score 10 (so far so good) but then encounters three high-score nodes 60,92,98 (Figure 18 e). Having failed to find any promising syntheses branching from node 5, the algorithm keeps 8and 10 as already visited, adds 60,61,76,91,92,98 to the PQ (which now comprises nodes 35,60,61,63,71,76,85,91,92,93,97,98) and moves to the best available PQ option. In this particular example,t his best option is the already explored endpoint 35.…”

Section: "Intelligent" Searchesmentioning

confidence: 99%

“…In this particular example,t his best option is the already explored endpoint 35. This endpoint is now expanded into nodes 56,68,73,88, of which the first is better than any entries in the PQ (now 60,61,63,68,71,73,76,85,88,91,92,93,97,98) (Figure 18 f). Accordingly,t he algorithm moves to 56 and expands it into options with scores 57, 64 and 77 (Figure 18 g).…”

Section: "Intelligent" Searchesmentioning

confidence: 99%

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Computer‐Assisted Synthetic Planning: The End of the Beginning

et al. 2016

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Exactly half a century has passed since the launch of the first documented research project (1965 Dendral) on computer-assisted organic synthesis. Many more programs were created in the 1970s and 1980s but the enthusiasm of these pioneering days had largely dissipated by the 2000s, and the challenge of teaching the computer how to plan organic syntheses earned itself the reputation of a "mission impossible". This is quite curious given that, in the meantime, computers have "learned" many other skills that had been considered exclusive domains of human intellect and creativity-for example, machines can nowadays play chess better than human world champions and they can compose classical music pleasant to the human ear. Although there have been no similar feats in organic synthesis, this Review argues that to concede defeat would be premature. Indeed, bringing together the combination of modern computational power and algorithms from graph/network theory, chemical rules (with full stereo- and regiochemistry) coded in appropriate formats, and the elements of quantum mechanics, the machine can finally be "taught" how to plan syntheses of non-trivial organic molecules in a matter of seconds to minutes. The Review begins with an overview of some basic theoretical concepts essential for the big-data analysis of chemical syntheses. It progresses to the problem of optimizing pathways involving known reactions. It culminates with discussion of algorithms that allow for a completely de novo and fully automated design of syntheses leading to relatively complex targets, including those that have not been made before. Of course, there are still things to be improved, but computers are finally becoming relevant and helpful to the practice of organic-synthetic planning. Paraphrasing Churchill's famous words after the Allies' first major victory over the Axis forces in Africa, it is not the end, it is not even the beginning of the end, but it is the end of the beginning for the computer-assisted synthesis planning. The machine is here to stay.

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Section: "Intelligent" Searchesmentioning

confidence: 99%

Section: "Intelligent" Searchesmentioning

confidence: 99%

Computer‐Assisted Synthetic Planning: The End of the Beginning

et al. 2016

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“…[42][43][44] The product mixture of the formose reaction was analyzed by multiple groups and more than 40 reaction products were identified to date. [37][38][39] We investigated the structures and properties of formose reaction networks obtained after 9…”

Section: Probing the Chemistry Of The Formose Reaction Networkmentioning

confidence: 99%

“…36,37 More than 40 compounds were experimentally identified as products of the formose reaction 38,39 and major pathways are known, 37,40 however many mechanistic details remain obscure. The formose reaction is one of the simplest organic reaction exhibiting autocatalysis 41 and was early conjectured as a potential route to sugars in the course of prebiotic evolution.…”

Section: Introductionmentioning

confidence: 99%

“…40,[42][43][44] We present models of the formose reaction in different stoichiometries obtained using a combination of chemical heuristics and semiempirical quantum chemistry (Section 3). The formose reaction models contained formose sugars up to C 5 known from experiments 38,39 and major reaction pathways postulated in the literature. 37,41 Furthermore, the reaction models obtained using heuristics-aided quantum chemistry permit analyses of chemical composition, energetics, and network structure, which are detailed in our companion publication.…”

Section: Introductionmentioning

confidence: 99%

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Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry

Rappoport

Galvin

Zubarev

et al. 2014

J. Chem. Theory Comput.

127

155

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While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here we present heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction of prebiotic evolution reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

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Computergestützte Syntheseplanung: Das Ende vom Anfang

et al. 2016

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Seit der Einführung des ersten dokumentierten Forschungsprojekts (Dendral, 1965) zur rechnergestützten organischen Synthese ist ein halbes Jahrhundert vergangen. In den 1970er und 1980er Jahren wurden viele weitere Programme entwickelt, doch bis zu den 2000er Jahren war der Enthusiasmus dieser Pionierzeit weitgehend verschwunden, und wegen der schwierigen Aufgabe, die Planung organischer Synthesen in Computer einzugeben, erhielt sie den Ruf einer “Mission impossible”. Das ist recht merkwürdig angesichts der Tatsache, dass Computer in der Zwischenzeit viele andere Fähigkeiten “gelernt” haben, die als alleinige Domänen von Intellekt und Kreativität des Menschen betrachtet wurden – so können Rechner heutzutage besser Schach spielen als menschliche Weltmeister, und sie können klassische Musik komponieren, die für das menschliche Ohr angenehm ist. In der organischen Synthese hat es zwar keine vergleichbaren Leistungen gegeben, aber dieser Aufsatz behauptet, dass es verfrüht wäre, eine Niederlage einzugestehen. Tatsächlich kann dem Computer schließlich “beigebracht” werden, die Synthesen von komplizierten organischen Verbindungen in Sekunden‐ bis Minutenschnelle zu planen, indem die Kombination aus moderner Rechenleistung und Algorithmen aus der Graphen‐/Netzwerktheorie zusammengeführt wird mit in geeigneten Formaten codierten chemischen Regeln (mit vollständiger Stereo‐ und Regiochemie) und Elementen der Quantenmechanik. Der Aufsatz beginnt mit einem Überblick über theoretische Grundkonzepte, die essenziell sind für die Analyse der großen Datenmengen chemischer Synthesen. Im Anschluss daran wird auf die Optimierung von Synthesewegen unter Einbeziehung bekannter Reaktionen eingegangen. Einen Schwerpunkt bildet die anschließende Besprechung der Algorithmen, die eine vollständig neue und automatisierte Planung der Synthesen für komplizierte Zielverbindungen ermöglichen, darunter auch solche, die noch nicht hergestellt wurden. Es gibt natürlich noch Verbesserungsmöglichkeiten, letztendlich aber werden Computer für die praktische Planung der organischen Synthese wichtig und hilfreich sein. Churchills berühmte Worte nach dem ersten wichtigen Sieg der Alliierten über die Achsenmächte paraphrasierend, ist es für die computergestützte Syntheseplanung nicht das Ende, nicht einmal der Anfang vom Ende, sondern das Ende vom Anfang. Der Computer ist da und wird bleiben.

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Accurate Analysis of Formose Reaction Products by LC–UV: An Analytical Challenge

Cited by 18 publications

References 17 publications

Computer‐Assisted Synthetic Planning: The End of the Beginning

Computer‐Assisted Synthetic Planning: The End of the Beginning

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry

Computergestützte Syntheseplanung: Das Ende vom Anfang

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