Quantum Isomer Search

Isomer search or molecule enumeration refers to the problem of finding all the isomers for a given molecule. Many classical search methods have been developed in order to tackle this problem. However, the availability of quantum computing architectures has given us the opportunity to address this problem with new (quantum) techniques. This paper describes a quantum isomer search procedure for determining all the structural isomers of alkanes. We first formulate the structural isomer search problem as a quadratic unconstrained binary optimization (QUBO) problem. The QUBO formulation is for general use on either annealing or gate-based quantum computers. We use the D-Wave quantum annealer to enumerate all structural isomers of all alkanes with fewer carbon atoms (n < 10) than Decane (C10H22). The number of isomer solutions increases with the number of carbon atoms. We find that the sampling time needed to identify all solutions scales linearly with the number of carbon atoms in the alkane. We probe the problem further by employing reverse annealing as well as a perturbed QUBO Hamiltonian and find that the combination of these two methods significantly reduces the number of samples required to find all isomers.Comment: 20 pages, 9 figure

Development of efficient open-source chemical graph generators

In chemistry, one of the crucial problems has been the structure identification of molecules, whose chemical composition is unknown. This research topic has impacts on various fields such as natural product and drug discovery studies. For the efficient and the fast identification process, computer assisted structure elucidation (CASE) toolkits has been developed. These tools utilise spectral data of unknown molecules as the input to determine their structure. The effectiveness of these software primarily depends on how well the structure generators perform. The basic input for these generators is the molecular formula of the unknown molecule to generate its unique list of isomers. In cheminformatics, there has been several software for the structure generation, especially, MOLGEN was considered as the de-facto gold standard in the field due to its speed and efficiency. However, it is a commercial tool and there was the need of an efficient open-source structure generators, in other words, chemical graph generators. To fulfil this need, the development of efficient open-source chemical graph generators was aimed for this PhD study, and the aim was succeeded by the development of two software, namely, MAYGEN and surge. First MAYGEN was developed as an alternative to MOLGEN. It was benchmarked against MOLGEN and was just around 3 times slower than MOLGEN. Following MAYGEN, another software, surge, was developed as an open-source chemical graph generator. It was benchmarked against MOLGEN for randomly chosen natural products&#39; molecular formulae. Based on the results, surge is approximately 100 times faster than MOLGEN, which made it the state-of-art in the field

Quantum computing and materials science: A practical guide to applying quantum annealing to the configurational analysis of materials

Using quantum computers for computational chemistry and materials science will enable us to tackle problems that are intractable on classical computers. In this paper, we show how the relative energy of defective graphene structures can be calculated by using a quantum annealer. This simple system is used to guide the reader through the steps needed to translate a chemical structure (a set of atoms) and energy model to a representation that can be implemented on quantum annealers (a set of qubits). We discuss in detail how different energy contributions can be included in the model and what their effect is on the final result. The code used to run the simulation on D-Wave quantum annealers is made available as a Jupyter Notebook. This Tutorial was designed to be a quick-start guide for the computational chemists interested in running their first quantum annealing simulations. The methodology outlined in this paper represents the foundation for simulating more complex systems, such as solid solutions and disordered systems

Quantum computing and materials science: A practical guide to applying quantum annealing to the configurational analysis of materials

Using quantum computers for computational chemistry and materials science will enable us to tackle problems that are intractable on classical computers. In this paper, we show how the relative energy of defective graphene structures can be calculated by using a quantum annealer. This simple system is used to guide the reader through the steps needed to translate a chemical structure (a set of atoms) and energy model to a representation that can be implemented on quantum annealers (a set of qubits). We discuss in detail how different energy contributions can be included in the model and what their effect is on the final result. The code used to run the simulation on D-Wave quantum annealers is made available as a Jupyter Notebook. This Tutorial was designed to be a quick-start guide for the computational chemists interested in running their first quantum annealing simulations. The methodology outlined in this paper represents the foundation for simulating more complex systems, such as solid solutions and disordered systems

The solid state structure and properties of stiff chain aramids

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1990.Includes bibliographical references (v. 2, leaves 185-191).by Gregory Charles Rutledge.Ph.D

Quantum computing and materials science : a practical guide to applying quantum annealing to the configurational analysis of materials

Using quantum computers for computational chemistry and materials science will enable us to tackle problems that are intractable on classical computers. In this paper, we show how the relative energy of defective graphene structures can be calculated by using a quantum annealer. This simple system is used to guide the reader through the steps needed to translate a chemical structure (a set of atoms) and energy model to a representation that can be implemented on quantum annealers (a set of qubits). We discuss in detail how different energy contributions can be included in the model and what their effect is on the final result. The code used to run the simulation on D-Wave quantum annealers is made available as a Jupyter Notebook. This Tutorial was designed to be a quick-start guide for the computational chemists interested in running their first quantum annealing simulations. The methodology outlined in this paper represents the foundation for simulating more complex systems, such as solid solutions and disordered systems

Theoretical Studies on Helical Polymer Modeling and Folding

Die Entdeckung der DNA-Doppelhelix bei Watson und Crick im Jahr 1953 war einer der wichtigsten Meilensteine in der Erforschung makromolekularer Strukturen. Diese Entdeckung führte zur Verfolgung zahlreicher Forschungslinien und Anwendungen, die sich mit der Faltung, Synthese und Strukturbestimmung von Helixstrukturen befassen. Heute ist weithin bekannt, dass Helices eine wichtige Rolle in Biomolekülen spielen, und es besteht ein großes Interesse an der Nutzung dieses Motivs in einem breiteren Spektrum von Anwendungen, z. B. in der Biomedizin und der Entwicklung von Soft Materials. Die vorliegende Arbeit basiert auf dem letztgenannten Bereich und konzentriert sich auf das Design helikaler Polymere aus theoretischer Sicht. Molekulare Simulationstechniken wie Molekulardynamik und Monte Carlo wurden bereits in großem Umfang zur Erforschung von Polymerstrukturen eingesetzt. Häufig werden diese Ansätze auf helikale Strukturen mit hohen Inversionsbarrieren angewandt oder erfordern experimentellen Struktureinsatz, um die Messungen zu reproduzieren. In dieser Arbeit verwenden wir rein theoretische Ansätze, um die treibenden Kräfte bei der Induktion dynamischer helikaler Polymere zu verstehen und helikale Konformationen von Polymeren zu modellieren. Zunächst wurden Erkenntnisse über die helikale Induktion von Poly-4-carboxyphenylacetylen durch chirale Amine mithilfe von DFT-Optimierungen, DFT-Dihedral-Scans und Molekulardynamik untersucht. Die DFT-Ergebnisse zeigen, dass die Geometrien der lokalen Wechselwirkung zwischen den chiralen Aminen und den Carboxygruppen des Polymers eine wichtige Rolle beim Induktionsprozess spielen. Die Bader-Ladungsanalyse zeigt unterschiedliche Ladungstransfers beim Vergleich von R- und S-Konformationen, die mit rechts- und linksdrehenden schraubenförmigen Polymeren. In der nächsten Arbeit wurden systematische Protokolle erstellt, um helikale Strukturen von post-modifizierten Polyphenylacetylenen durch chirale Amine zu modellieren. Dies wurde sowohl für para- als auch für meta-substituierte Seitenketten durchgeführt. Es wurden blinde und lokale Helix-Suchen auf der Grundlage von Monte-Carlo-Simulationen und DFT-Dihedral-Scans verwendet. Als wichtigste stabilisierende Wechselwirkungen erwiesen sich H-Bindungen, $\pi - \pi$ Stapelwechselwirkungen und $\pi - \pi$ T-förmige Wechselwirkungen. Im letzten Kapitel wurde ein de novo Design von helikalen Strukturen unter Verwendung von sequenzgesteuerten Oligomeren durchgeführt. Es wurden Monte-Carlo-Simulationen durchgeführt, und das helikale Design wurde durch eine Wasserstoffbrücken-Clusteranalyse geleitet. Es wurden verschiedene Klassen von Sequenzen mit unterschiedlichen Längen der Rückgrate und Seitenkettenmodifikationen berücksichtigt. Die besten helikalen Sequenzen wurden mit Molekulardynamik mit einem expliziten Lösungsmittel simuliert, um ihre Stabilität zu testen

Genetische Algorithmen in der Theoretischen Chemie : Entwicklung und Anwendungen eines allgemeinen Frameworks.

Die vorliegende Arbeit beschreibt die Entwicklung und Andwendungen eines allgemeinen Frameworks zur globalen Optimierung von theoretisch-chemischen Problemstellungen mittels genetischer Algorithmen. Als Anwendungen des Frameworks werden die Strukturoptimierung gemischter Cluster, die Parametrisierung von Potentialen gegen Referenzdaten und das molekulare Design schaltbarer Molekuele gezeigt