DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules

Abstract

A general-purpose software package, termed DE Novo OPTimization of In/organic Molecules (DENOPTIM), for de novo design and virtual screening of functional molecules is described. Molecules of any element and kind, including metastable species and transition states, are handled as chemical objects that go beyond valence-rules representations. Synthetic accessibility of the generated molecules is ensured via detailed control of the kinds of bonds that are allowed to form in the automated molecular building process. DENOPTIM contains a combinatorial explorer for screening and a genetic algorithm for global optimization of user-defined properties. Estimates of these properties may be obtained to form the fitness function (figure of merit or scoring function) from external molecular modeling programs via shell scripts. Examples of a range of different fitness functions and DENOPTIM applications, including an easy-to-do test case, are described. DENOPTIM is available as Open Source from .

Computational Discovery of Transition-metal Complexes: From High-throughput Screening to Machine Learning

“…Jensen and co-workers developed the DENOPTIM code to enable evolutionary-algorithm-based design of transition-metal complexes from fragments, building upon several other earlier tools (e.g., the fragment explorer) with wrapper codes (Figure ). DENOPTIM represents the molecule as a graph, and the code analyzes fragments in the molecule by comparison to available databases (e.g., ChEMBL and the CSD).…”

“…Jensen and co-workers developed the DENOPTIM code to enable evolutionary-algorithm-based design of transition-metal complexes from fragments, building upon several other earlier tools (e.g., the fragment explorer) with wrapper codes (Figure ). DENOPTIM represents the molecule as a graph, and the code analyzes fragments in the molecule by comparison to available databases (e.g., ChEMBL and the CSD). Mutations to the fragments of the complex are carried out through a series of routines that ensure synthetic accessibility while optimizing for the user-provided fitness function (Figure ).…”

Unlocking the computational design of metal–organic cages

“…5a ). 95 There are also multiple software for generating 3D coordinates of transition metal complexes and to perform de novo generation 103 of metal complexes: DENOPTIM, 104 molSimplify 105 and Molassembler . 106 For the organic components, free software like RDKit 97,107,108 or Open Babel 61 can easily generate 3D conformers from 2D representations of molecules.…”

Selective production of linear α-olefins via catalytic deoxygenation of fatty acids and derivatives

“…This tool identifies potential candidates by optimizing a fitness based on key parameters (descriptors), where the optimization is done by combining molecular fragments trough an automated evolutionary algorithm, and has already been used to identify new complexes. 180 Hopefully, with the now deeper understanding of the mechanism of decarbonylative dehydration, an automated catalyst prediction process is not too far away.…”