Analyzing Learned Molecular Representations for Property Prediction

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows

Quanten-chemische Beschreibung von ultraschnellem Self-trapping von Exzitonen in Perylen-basierten Materialien

Im Rahmen dieser Dissertation wurden sehr lange Exzitonen-Diffusionslängen (LD) unter idealen Bedingungen für Perylen-basierte Materialien simuliert. Dies ist ein Indiz dafür, dass die sehr kurzen LD in realen Materialien aus einer extrinsischen sowie einer intrinsischen Immobilisierung resultieren. Letztere basiert auf einer Relaxation in sogenannten „Self-Trapping“-Zustände. Ein tieferes Verständnis der dem Self-Trapping zugrunde liegenden atomistischen Prozesse ist notwendig, um zukünftig Materialien mit langen LD entwickeln zu können, bei denen eine intrinsische Exzitonen-Immobilisierung verhindert wird. Für die Entwicklung eines solchen mechanistischen Verständnisses ist das Vorliegen einer eindeutigen Korrelation zwischen der molekularen Anordnung und der LD unabdingbar. Diese weisen Einkristalle von Diindenoperylen (DIP) und α-Perylen-tetracarboxyl-anhydrid (α-PTCDA) auf. Bei ersteren wurde eine außergewöhnlich lange LD von 90 nm und bei letzteren nur 22 nm gemessen. Teil dieser Arbeit war es, Gründe für diesen Unterschied in der LD zu finden. Nur Self-Trapping kommt als Ursache in Frage. Aus diesem Grund eignen sich diese Materialien, um ein atomistisches Verständnis des Self-Trappings exemplarisch an ihnen zu erarbeiten. Mutmaßlich könnten Differenzen in der elektronischen Struktur in DIP und α-PTCDA für das unterschiedliche Self-Trapping verantwortlich sein. Allerdings konnte gezeigt werden, dass es für viele Perylen-basierte Materialien keine signifikanten Unterschiede in der elektronischen Struktur gibt, wodurch diese für die Aufklärung von Immobilisierungsmechanismen zu vernachlässigen sind. Eine weitere mögliche Begründung wäre in Polarisationseffekten im Kristall zu suchen, welche die elektronische Struktur in Perylen-basierten Materialien unterschiedlich beeinflussen. Vor allem ihr Einfluss auf Ladungstrennungs-Zustände (CT), die oberhalb des optisch hellen Frenkel-Zustandes liegen, war fraglich, weil sie energetisch abgesenkt werden könnten. Ein signifikanter Einfluss von Polarisationseffekten konnte aber für alle Zustände mittels eines polarisierbaren Kontinuum-Modells ausgeschlossen werden. Die geringe LD im α-PTCDA ist folglich ein Indiz für ein Self-Trapping, das durch die Kristallstruktur aus π-Stapeln evoziert wird, welche in DIP fischgrätenartig ist. Da Polarisationseffekte auszuschließen sind, übt der Kristall lediglich durch sterische Restriktionen einen Einfluss auf das Dimer aus. Daher muss die Methode für die Beschreibung von Self-Trapping nur diese Effekte berücksichtigen, so dass sich für den Einsatz des mechanical embedding QM/MM-Ansatzes entschieden wurde. Nun konnten Potentialflächen berechnet werden, auf denen anschließend eine Wellenpaketdynamik durchgeführt wurde. Diese Methode erlaubt es erstmals, Mechanismen der Exzitonen-Immobilisierung in organischen Materialien auf einer atomistischen Ebene zu beschreiben. Als Erklärung für Self-Trapping in α-PTCDA dienten Potentialflächen, die eine intermolekulare Verschiebung des Dimers im Kristall abbilden. So wurde eine Exzitonen-Immobilisierung innerhalb von 500 fs gefunden, die aus einem irreversiblem Energieverlust und einer lokalen Verzerrung der Kristallstruktur resultiert und auf diese Weise den weiteren Transport des Exzitons verhindert. Im Fall von DIP kann diese Immobilisierung aufgrund hoher Energiebarrieren nicht stattfinden. Diese Barrieren resultieren aus der fischgrätenartigen Kristallstruktur des DIP. Diese Diskrepanzen in der Dynamik erklären die unterschiedlichen LD-Werte für DIP und α-PTCDA. In einem weiteren Fall wurde eine Exzitonen-Immobilisierung in helikalen π Aggregaten von Perylen-tetracarboxyl-bisimid (PBI) Molekülen festgestellt. Hier wird Self-Trapping durch einen Relaxationsmechanismus verursacht, in dem das Exziton durch geringe asymmetrische Schwingungen des Aggregats innerhalb von 200 fs von dem hellen Frenkel- in den dunklen Frenkel-Zustand transferiert wird, wobei dieser Übergang von einem CT-Zustand vermittelt wird. Der gesamte Vorgang ist nur bei helikalen Aggregaten möglich, weil nur hier CT-Zustände sehr dicht bei dem hellen Frenkel-Zustand vorhanden sind. Im finalen Frenkel-Zustand tritt eine Torsionsbewegung um die π-Stapelachse ein, so dass ein Energieverlust und eine lokale Änderung der Aggregatstruktur erfolgt – also ein Self-Trapping des Exzitons. Dieser modellierte Mechanismus steht im Einklang zu allen vorliegenden experimentellen Daten. Diese Erkenntnisse lassen die Schlussfolgerung zu, dass in künftigen Materialen für organische Solarzellen eine irreversible und ultraschnelle Deformation des Aggregats nach der Photoanregung vermieden werden muss - will man lange LD erreichen. Nur so kann Self-Trapping von Exzitonen verhindert werden.In the context of this dissertation very long ranged exciton diffusion lengths (LD) were simulated for perylene-based materials under ideal conditions. This leads to the conclusion that the short LD values in existing materials result from an extrinsic and intrinsic immobilization. The latter, which is a specific material property, is based on a relaxation of the exciton into self-trapping states. An in-depth understanding of the atomistic processes defining self-trapping is essential to developing materials with long LD in the future, in which intrinsic immobilization is prevented. For the development of such a mechanistic understanding it is crucial that a clear relationship between molecular structure and LD is available. This is given by single crystals of diindeno perylene (DIP) and α-perylene tetracarboxylic anhydride (α-PTCDA). An extraordinary large LD of 90 nm was measured for the first one, while the latter possesses only 22 nm. Part of this thesis was to deliver reasons for this discrepancy. Only self-trapping comes into question to explain the different LD values. One reason for the different self-trapping in DIP and α-PTCDA could lie in the electronic structure. However, it was possible to demonstrate that a wide range of perylene-based materials possess no significant differences in their electronic structures. Consequently, such differences can be neglected for the explanation of immobilization mechanisms for the exciton. A further possible explanation could be polarization effects in the crystal, which influences the electronic structure of perylene based materials differently. Especially their influence on charge transfer (CT) states, which are located above the optically bright Frenkel state, was in question because such states could be stabilized by a polarizable surrounding. A significant influence of polarization effects on all considered states were excluded by using a polarizable continuum model. Hence, the small LD values in α-PTCDA are an evidence for self-trapping, which produces a crystal structure built up by π-stacks, while the one of DIP is of herringbone type. Since polarization effects can be neglected, is the dimer only via steric restrictions influenced by the crystal. Hence, a method describing self-trapping has to consider such effects, so that a mechanical embedding QM/MM approach is sufficient. Now, potential energy surfaces were calculated, on which wave packet dynamics were subsequently performed. In this way, atomistic mechanisms for the immobilization of excitons were described for the first time in organic materials. Self-trapping was studied in crystals of α-PTCDA by potential energy surfaces, which map an intermolecular shift motion of the dimer in the crystal. An immobilization of excitons occurs within 500 fs, which results from an irreversible energy loss together with a local deformation of the crystal lattice. This prevents a further transport of the exciton. In the case of DIP, this immobilization does not proceed due to high barriers. These barriers result from the herringbone type packing motif in the DIP crystal. This discrepancy in the dynamics explains the different LD values in DIP and α-PTCDA. In a further example, an exciton immobilization was found in helical π-aggregates of perylene tetracarboxylic bisimide (PBI) molecules. Self-trapping is caused by a relaxation mechanism, in which the exciton is transferred by asymmetric vibrations of the aggregate from the bright to a dark Frenkel state within 200 fs, whereby the transition is mediated by a CT state. However, the CT state is almost non-populated during the whole mechanism so that its participation could not yet be proven experimentally. This entire procedure is solely possible in helical aggregates, because only for such structures is there a CT state located next to the bright Frenkel state. At the final Frenkel state a torsional motion around the π-stacking axis is possible so that the loss in energy and the local rearrangement of the aggregate structure occurs, which means a self-trapping of the exciton. This mechanism is in perfect agreement with all available experimental data. These insights allow the conclusion that in future materials for organic solar cells an irreversible and ultrafast deformation of aggregates after photo-absorption must be avoided. Only in this way long LD values can be achieved and exciton self-trapping can be prevented. However, small LD values are always predicted in helical aggregates of perylene-based materials, because exciton immobilization occurs already due to small molecular motions. For this reason such aggregates are inappropriate for the use in organic solar cells. Long LD values are expected for aggregate structures with long intermolecular shifts or molecules with bulky substituents

A computational study of the methanolysis of palladium-acyl bonds

Density functional calculations suggest that intermolecular attack of methanol may be important in the methanolysis of simple Pd-acyl systems and that the energetics of this process are strongly dependent on the metal coordination environment.</p

Dataset for "ConfSolv: Prediction of solute conformer free energies across a range of solvents"

&lt;p&gt;This dataset contains three archives. The first archive, full_dataset.zip, contains&nbsp;geometries and free energies&nbsp;for nearly 44,000 solute molecules with almost 9 million conformers, in 42 different solvents. The geometries and gas phase free energies are computed using density functional theory (DFT). The solvation free energy for each conformer is computed&nbsp;using&nbsp;COSMO-RS and the solution free energies are computed using the sum of the gas phase free energies and the solvation free energies. The geometries for each solute conformer are provided as ASE_atoms_objects within a pandas DataFrame, found in the compressed file&nbsp;dft coords.pkl.gz within full_dataset.zip. The gas-phase energies, solvation free energies, and solution free energies are also provided as a pandas DataFrame in the compressed file free_energy.pkl.gz within full_dataset.zip. Ten example data splits for both random and scaffold split types are also provided in the ZIP archive&nbsp;for&nbsp;training models. Scaffold split index 0 is used to generate results in the corresponding publication.&nbsp;&lt;/p&gt;&lt;p&gt;The second archive, refined_conf_search.zip, contains geometries and free energies for a representative sample of 28 solute molecules from the full dataset that were subject to a refined conformer search and thus had more conformers located. The format of the data is identical to full_dataset.zip.&lt;/p&gt;&lt;p&gt;The third archive contains one folder for each solvent for which we have provided free energies in full_dataset.zip. Each folder contains the .cosmo file for every solvent conformer used in the COSMOtherm calculations, a dummy input file for the COSMOtherm calculations, and a CSV file that contains the electronic energy of each solvent conformer that needs to be substituted for "EH_Line" in the dummy input file.&lt;/p&gt

Ultrafast Exciton Self-Trapping upon Geometry Deformation in Perylene-Based Molecular Aggregates

Femtosecond time-resolved experiments demonstrate that the photoexcited state of perylene tetracarboxylic acid bisimide (PBI) aggregates in solution decays nonradiatively on a time-scale of 215 fs. High-level electronic structure calculations on dimers point toward the importance of an excited state intermolecular geometry distortion along a reaction coordinate that induces energy shifts and couplings between various electronic states. Time-dependent wave packet calculations incorporating a simple dissipation mechanism indicate that the fast energy quenching results from a doorway state with a charge-transfer character that is only transiently populated. The identified relaxation mechanism corresponds to a possible exciton trap in molecular materials

Identification of Ultrafast Relaxation Processes As a Major Reason for Inefficient Exciton Diffusion in Perylene-Based Organic Semiconductors

The exciton diffusion length (<i>L</i>_D) is a key parameter for the efficiency of organic optoelectronic devices. Its limitation to the nm length scale causes the need of complex bulk-heterojunction solar cells incorporating difficulties in long-term stability and reproducibility. A comprehensive model providing an atomistic understanding of processes that limit exciton trasport is therefore highly desirable and will be proposed here for perylene-based materials. Our model is based on simulations with a hybrid approach which combines high-level ab initio computations for the part of the system directly involved in the described processes with a force field to include environmental effects. The adequacy of the model is shown by detailed comparison with available experimental results. The model indicates that the short exciton diffusion lengths of α-perylene tetracarboxylicdianhydride (PTCDA) are due to ultrafast relaxation processes of the optical excitation via intermolecular motions leading to a state from which further exciton diffusion is hampered. As the efficiency of this mechanism depends strongly on molecular arrangement and environment, the model explains the strong dependence of <i>L</i>_D on the morphology of the materials, for example, the differences between α-PTCDA and diindenoperylene. Our findings indicate how relaxation processes can be diminished in perylene-based materials. This model can be generalized to other organic compounds

Analyzing Learned Molecular Representations for Property Prediction

© 2019 American Chemical Society. Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial data sets spanning a wide variety of chemical end points. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary data sets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows

The conformations of 13-vertex ML₂C₂B₁₀ metallacarboranes:experimental and computational studies

The docosahedral metallacarboranes 4,4-(PMe2Ph) 2-4,1,6-closo-PtC2B10H12, 4,4-(PMe2Ph)2-4,1,10-closo-PtC2B 10H12, and [N(PPh3)2][4,4-cod-4,1, 10-closo-RhC2B10H12] were prepared by reduction/ metalation of either 1,2-closo-C2B10H 12 or 1,12-closo-C2B10H12. All three species were fully characterized, with a particular point of interest of the latter being the conformation of the {ML2} fragment relative to the carborane ligand face. Comparison with conformations previously established for six other ML2C2B10 species of varying heteroatom patterns (4,1,2-MC2B10, 4,1,6-/WC2Bi0, 4,1,10-MC2B10, and 4,1,12-MC2B10) reveals clear preferences. In all cases a qualitative understanding of these was afforded by simple MO arguments applied to the model heteroarene complexes [(PH3)2PtC2B4H6] 2- and [(PH3)2PtCB5H 6]3-. Moreover, DFT calculations on [(PH3) 2PtC2B4H6]2 in its various isomeric forms approximately reproduced the observed conformations in the 4,1,2-, 4,1,6-, and 4,1,10-MC2B10 species, although analogous calculations on [(PH3)2PtCB5H 6]3- did not reproduce the conformation observed in the 4,1,12-MC2B10 metallacarborane. DFT calculations on (PH3)2PtC2B10H12 yielded good agreement with experimental conformations in all four isomeric cases. Apparent discrepancies between observed and computed Pt-C distances were probed by further refinement of the 4,1,2- model to 1,2-(CH2) 3-4,4-(PMe3)2-4,1,2-closo-PtC2B 10H10. This still has a more distorted structure than measured experimentally for 1,2-(CH2)3-4,4-(PMe 2Ph)2-4,1,2-closo-PtC2B10H 10, but the structural differences lie on a very shallow potential energy surface. For the model compound a henicosahedral transition state was located 8.3 kcal mol-1 above the ground-state structure, consistent with the fluxionality of 1,2-(CH2)3-4,4-(PMe 2Ph)2-4,1,2-closo-PtC2B10H 10 in solution.</p