Data-driven tailoring of molecular dipole polarizability and frontier orbital energies in chemical compound space

Góger, Szabolcs; Sandonas, Leonardo Medrano; Müller, Carolin; Tkatchenko, Alexandre

doi:10.1039/d3cp02256k

Cited by 6 publications

(6 citation statements)

References 94 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To understand the relevance of accessing to QM data for solvated molecules, we first discuss the influence of implicit water on extensive and intensive molecular QM properties. In doing so, as an illustrative example, we have analyzed the 2D property space defined by two contrasting properties 90,91 such as the isotropic molecular polarizability α and the HOMO-LUMO gap E gap (i.e., α, E gap -space) for the 59, 783 conformations in AQM-gas and AQM-sol as well as the set of most stable conformer per molecule in AQM-sol (only 1, 653 conformations), see Fig. 4(a).…”

Section: Technical Validationmentioning

confidence: 99%

“…4(b). Accordingly, these findings could carry crucial implications in the "freedom of design" when searching for large drug-like molecules with targeted α, E gap values [90][91][92] . Notice that the conformational sampling per molecule largely improved the coverage of both properties, connecting isolated regions associated with a single molecular structure with specific size and chemical composition.…”

Section: Technical Validationmentioning

confidence: 99%

See 1 more Smart Citation

Aquamarine: Quantum-Mechanical Exploration of Conformers and Solvent Effects in Large Drug-like Molecules

Medrano Sandonas,

Van Rompaey,

Fallani

et al. 2024

Preprint

View full text Add to dashboard Cite

We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean:50.9), and containing up to 54 (mean:28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global (molecular) and local (atom-in-a-molecule) physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and \textit{de novo} generation of large (solvated) molecules with pharmaceutical and biological relevance.

show abstract

Section: Technical Validationmentioning

confidence: 99%

Section: Technical Validationmentioning

confidence: 99%

Aquamarine: Quantum-Mechanical Exploration of Conformers and Solvent Effects in Large Drug-like Molecules

Medrano Sandonas,

Van Rompaey,

Fallani

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…To understand the relevance of accessing QM data for solvated molecules, we first discuss the influence of implicit water on extensive and intensive molecular QM properties. In doing so, as an illustrative example, we have analyzed the 2D property space defined by two contrasting properties 98 , 99 such as the isotropic molecular polarizability α and the HOMO-LUMO gap E gap ( i.e ., -space) for the 59, 783 conformations in AQM-gas and AQM-sol as well as the set of most stable conformer per molecule in AQM-sol (only 1, 653 conformations), see Fig. 4(a) .…”

Section: Technical Validationmentioning

confidence: 99%

“…4(b) . Accordingly, these findings could carry crucial implications in the “freedom of design” when searching for large drug-like molecules with targeted values 98 – 100 . Notice that the conformational sampling per molecule largely improved the coverage of both properties, connecting isolated regions associated with a single molecular structure with specific size and chemical composition.…”

Section: Technical Validationmentioning

confidence: 99%

Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules

Medrano Sandonas,

Van Rompaey,

Fallani

et al. 2024

Sci Data

View full text Add to dashboard Cite

We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean: 50.9), and containing up to 54 (mean: 28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global and local physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and de novo generation of large (solvated) molecules with pharmaceutical and biological relevance.

show abstract

“…For many-electron cases, the calculation of polarizability is based on evaluating the change of the dipole moment with respect to an external electric field or on the ability to accurately predict excited-state wave functions with methods such as time-dependent density functional theory or linear response coupled cluster theory. − Approaches using finite-field derivatives suffer from convergence and algorithmic issues, while excited-state calculations require excessive computational power. Therefore, calculating the dipole polarizability is still a demanding task in practice, which makes approximate methods, property correlations, and general scaling laws desirable. − …”

Section: Introductionmentioning

confidence: 99%

Four-Dimensional Scaling of Dipole Polarizability: From Single-Particle Models to Atoms and Molecules

Góger,

Karimpour,

Tkatchenko

2024

J. Chem. Theory Comput.

View full text Add to dashboard Cite

Scaling laws enable the determination of physicochemical properties of molecules and materials as a function of their size, density, number of electrons or other easily accessible descriptors. Such relations can be counterintuitive and nonlinear, and ultimately yield much needed insight into quantum mechanics of many-particle systems. In this work, we show on the basis of singleparticle models, multielectron atoms and molecules that the dipole polarizability of quantum systems is generally proportional to the fourth power of a characteristic length, computed from the ground-state wave function. This four-dimensional (4D) scaling is independent of the ratio of bound-to-bound and bound-tocontinuum electronic transitions and applies to many-electron atoms when a correlated length metric is used. Finally, this scaling law is applied to predict the polarizability of molecules by electrostatically coupled atoms-in-molecules approach, obtaining approximately 8% absolute and relative accuracy with respect to hybrid density functional theory (DFT) on the QM7−X data set of organic molecules, providing an efficient and scalable model for the anisotropic polarizability tensors of extended (bio)molecules.

show abstract

Data-driven tailoring of molecular dipole polarizability and frontier orbital energies in chemical compound space

Abstract: Using the extended QM7-X dataset, it is shown that polarizabilty and HOMO–LUMO gap are uncorrelated in the chemical compound space. The lack of correlation enables the design of novel materials, demonstrated through organic photodetector candidates.

Cited by 6 publications

References 94 publications

Aquamarine: Quantum-Mechanical Exploration of Conformers and Solvent Effects in Large Drug-like Molecules

Aquamarine: Quantum-Mechanical Exploration of Conformers and Solvent Effects in Large Drug-like Molecules

Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules

Four-Dimensional Scaling of Dipole Polarizability: From Single-Particle Models to Atoms and Molecules

Contact Info

Product

Resources

About