fromage: A library for the study of molecular crystal excited states at the aggregate scale

The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the interm...

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Vydáno v:	Journal of computational chemistry Ročník 41; číslo 10; s. 1045 - 1058
Hlavní autoři:	Rivera, Miguel, Dommett, Michael, Sidat, Amir, Rahim, Warda, Crespo‐Otero, Rachel
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Hoboken, USA John Wiley & Sons, Inc 15.04.2020 Wiley Subscription Services, Inc
Témata:	Aggregates Excitation exciton Excitons molecular aggregate Obstacle avoidance ONIOM Organic chemistry photochemistry Python library Software and Updates molecular aggregate ONIOM Python library exciton photochemistry
ISSN:	0192-8651, 1096-987X, 1096-987X
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Abstract	The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready‐to‐use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage. Accurately modeling the photoexcitations of molecular aggregates involves complementing excited state methodologies with auxiliary calculations. Due to the diversity of chemical and structural space in multimolecular complexes, these calculations require a high degree of adaptability which calls for the use of modular programming tools hitherto unavailable for the investigation of photochemical properties of molecular aggregates. The FRamewOrk for Molecular AGgregate Excitations (fromage), described herein, compiles geometry manipulation tools, exciton state characterization, and QM:QM′ models for geometry optimization.
AbstractList	The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in-house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready-to-use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage.The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in-house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready-to-use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage. The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready‐to‐use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage. The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready‐to‐use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage. Accurately modeling the photoexcitations of molecular aggregates involves complementing excited state methodologies with auxiliary calculations. Due to the diversity of chemical and structural space in multimolecular complexes, these calculations require a high degree of adaptability which calls for the use of modular programming tools hitherto unavailable for the investigation of photochemical properties of molecular aggregates. The FRamewOrk for Molecular AGgregate Excitations (fromage), described herein, compiles geometry manipulation tools, exciton state characterization, and QM:QM′ models for geometry optimization. The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready‐to‐use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage . The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready‐to‐use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage. Accurately modeling the photoexcitations of molecular aggregates involves complementing excited state methodologies with auxiliary calculations. Due to the diversity of chemical and structural space in multimolecular complexes, these calculations require a high degree of adaptability which calls for the use of modular programming tools hitherto unavailable for the investigation of photochemical properties of molecular aggregates. The FRamewOrk for Molecular AGgregate Excitations (fromage), described herein, compiles geometry manipulation tools, exciton state characterization, and QM:QM′ models for geometry optimization.
Author	Dommett, Michael Crespo‐Otero, Rachel Rivera, Miguel Sidat, Amir Rahim, Warda
AuthorAffiliation	1 Department of Chemistry, School of Biological and Chemical Sciences Queen Mary University of London London UK
AuthorAffiliation_xml	– name: 1 Department of Chemistry, School of Biological and Chemical Sciences Queen Mary University of London London UK
Author_xml	– sequence: 1 givenname: Miguel orcidid: 0000-0003-3699-2403 surname: Rivera fullname: Rivera, Miguel organization: Queen Mary University of London – sequence: 2 givenname: Michael surname: Dommett fullname: Dommett, Michael organization: Queen Mary University of London – sequence: 3 givenname: Amir surname: Sidat fullname: Sidat, Amir organization: Queen Mary University of London – sequence: 4 givenname: Warda surname: Rahim fullname: Rahim, Warda organization: Queen Mary University of London – sequence: 5 givenname: Rachel orcidid: 0000-0002-8725-5350 surname: Crespo‐Otero fullname: Crespo‐Otero, Rachel email: r.crespo-otero@qmul.ac.uk organization: Queen Mary University of London
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Keywords	molecular aggregate ONIOM Python library exciton photochemistry
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Snippet	The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the...
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SubjectTerms	Aggregates Excitation exciton Excitons molecular aggregate Obstacle avoidance ONIOM Organic chemistry photochemistry Python library Software and Updates
Title	fromage: A library for the study of molecular crystal excited states at the aggregate scale
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