Molecular Geometry Impact on Deep Learning Predictions of Inverted Singlet-Triplet Gaps.

We present a deep learning model able to predict excited singlet-triplet gaps with a mean absolute error (MAE) of ≈20 meV to obtain potential inverted singlet-triplet (IST) candidates. We exploit cutting-edge spherical message passing graph neural networks designed specifically for generating 3D graph representations in molecular learning. In a nutshell, the model takes as input a list of unsaturated heavy atom Cartesian coordinates and atomic numbers, producing singlet-triplet gaps as output. We exploited available large data collections to train the model on ≈40,000 heterogeneous density functional theory (DFT) geometries with available ADC(2)/cc-pVDZ singlet-triplet gaps. We ascertain the predictive power of the model from a quantitative perspective obtaining predictions on a test set of ≈14,000 molecules, whose geometries have been generated at DFT level (the same employed for the geometries in the training set), at GFN2-xTB level, and through Molecular Mechanics. We notice performance degradation upon switching to lower-quality geometries, with GFN2-xTB ones maintaining satisfactory results (MAE ≈ 50 meV on GFN2-xTB geometries, MAE ≈ 180 meV on generalized AMBER force field geometries), hinting at caution when dealing with specific chemical classes. Finally, we verify the performance of the model from the qualitative point of view, obtaining predictions on a different data set of ≈15,000 molecules already used to identify new IST molecules. We obtained predictions using both DFT and experimental X-ray geometries, with results on IST candidates similar to those provided by quantum chemical methods, with clear hints for the path toward improved performance.

Formation of electron traps in semiconducting polymers via a slow triple-encounter between trap precursor particles.

Already in 2012, Blom et al. reported (Nature Materials 2012, 11, 882) in semiconducting polymers on a general electron-trap density of ≈3 × 1017 cm-3, centered at an energy of ≈3.6 eV below vacuum. It was suggested that traps have an extrinsic origin, with the water-oxygen complex [2(H2O)-O2] as a possible candidate, based on its electron affinity. However, further evidence is lacking and the origin of universal electron traps remained elusive. Here, in polymer diodes, the temperature-dependence of reversible electron traps is investigated that develop under bias stress slowly over minutes to a density of 2 × 1017 cm-3, centered at an energy of 3.6 eV below vacuum. The trap build-up dynamics follows a 3rd-order kinetics, in line with that traps form via an encounter between three diffusing precursor particles. The accordance between universal and slowly evolving traps suggests that general electron traps in semiconducting polymers form via a triple-encounter process between oxygen and water molecules that form the suggested [2(H2O)-O2] complex as the trap origin.

Formation of universal electron traps in polymer light-emitting diodes is a dynamic process that occurs via a slow triple-encounter between trap precursor species, with the water-oxygen [2(H₂O)-O₂] complex as a likely candidate.

Identification of Unknown Inverted Singlet-Triplet Cores by High-Throughput Virtual Screening.

Molecules where the energy of the lowest excited singlet state is found below the energy of the lowest triplet state (inverted singlet-triplet molecules) are extremely rare. It is particularly challenging to discover new ones through virtual screening because the required wavefunction-based methods are expensive and unsuitable for high-throughput calculations. Here, we devised a virtual screening approach where the molecules to be considered with advanced methods are pre-selected with increasingly more sophisticated filters that include the evaluation of the HOMO-LUMO exchange integral and approximate CASSCF calculations. A final set of 7 candidates (0.05% of the initial 15 000) were verified to possess inversion between singlet and triplet states with state-of-the-art multireference methods (MS-CASPT2). One of them is deemed of particular interest because it is unrelated to other proposals made in the literature.

Shortwave infrared-absorbing squaraine dyes for all-organic optical upconversion devices.

Shortwave infrared (SWIR) optical sensing and imaging are essential to an increasing number of next-generation applications in communications, process control or medical imaging. An all-organic SWIR upconversion device (OUC) consists of an organic SWIR sensitive photodetector (PD) and an organic light-emitting diode (OLED), connected in series. OUCs directly convert SWIR to visible photons, which potentially provides a low-cost alternative to the current inorganic compound-based SWIR imaging technology. For OUC applications, only few organic materials have been reported with peak absorption past 1000 nm and simultaneous small absorption in the visible. Here, we synthesized a series of thermally stable high-extinction coefficient donor-substituted benz[cd]indole-capped SWIR squaraine dyes. First, we coupled the phenyl-, carbazole-, and thienyl-substituted benz[cd]indoles with squaric acid (to obtain the SQ dye family). We then combined these donors with the dicyanomethylene-substituted squaraine acceptor unit, to obtain the dicyanomethylene-functionalized squaraine DCSQ family. In the solid state, the absorbance of all dyes extended considerably beyond 1100 nm. For the carbazole- and thienyl-substituted DCSQ dyes, even the peak absorptions in solution were in the SWIR, at 1008 nm and 1014 nm. We fabricated DCSQ PDs with an external photon-to-current efficiency over 30%. We then combined the PD with a fluorescent OLED and fabricated long-term stable OUCs with peak sensitivity at 1020 nm, extending to beyond 1200 nm. Our OUCs are characterized by a very low dark luminance (<10-2 cd m-2 at below 6 V) in the absence of SWIR light, and a low turn-on voltage of 2 V when SWIR light is present.

Amplification of the chiroptical response of UV-transparent amines and alcohols by N-phthalimide derivatization enabling absolute configuration determination through ECD computational analysis.

The stereoselective transformation of chiral UV-transparent amines and alcohols to phthalimides has proved to be a simple and efficient method to enhance the chiroptical response of these substrates allowing their reliable absolute configuration determination by computational analysis of ECD spectra. Such a transformation also leads to a significant reduction in the molecular conformational flexibility thus simplifying the conformational analysis required by the computational treatment. The method described herein thus allows the absolute configuration assignment to these challenging substrates to be much easier and reliable.

On the arrangement of chromophores in light harvesting complexes: chance versus design.

We used a homogeneous computational approach to derive the excitonic Hamiltonian for five light harvesting complexes containing only one type of chromophore and compare them in terms of statistical descriptors. We then studied the approximate exciton dynamics for the five complexes introducing a measure, the (averaged and time-dependent) inverse participation ratio, that enables the comparison between very diverse complexes on the same ground. We find that the global dynamics are very similar across the set of systems despite the variety of geometric structures of the complexes. In particular, the dynamics of four out of five light harvesting complexes are barely distinguishable with a small variation from the norm seen only for the Fenna-Matthews-Olson complex. We use the information from the realistic Hamiltonians to build a reduced model system that shows how the global dynamics are ultimately dominated by a single parameter, the degree of localization of the excitonic Hamiltonian eigenstates. Considering the physically plausible range of system parameters, the reduced model explains why the dynamics are so similar across most light harvesting complexes containing a single type of chromophore regardless of the detailed pattern of the inter-chromophore excitonic coupling.

How fine-tuned for energy transfer is the environmental noise produced by proteins around biological chromophores?

We investigate the role of the local protein environment on the energy transfer processes in biological molecules, excluding from the analysis the effect of intra-chromophore nuclear motions, and focussing on the exciton-phonon coupling. We studied three different proteins (FMO and two variants of the WSCP protein) with different biological functions but similar chromophores, to understand whether a classification of chromophores based on the details of the environment would be possible, and whether specific environments enhance or suppress the coupling between exciton and protein dynamics. Our results show that despite the different biological role, there is no significant difference in the influence of the environment on the properties of the chromophores. Additionally, we show that the main role in influencing molecular properties is played by solvent molecules: the interaction occurs on a medium-range scale, and the solvent is kept in place by a strong H-bond network being free to rotate, suggesting a dipole-dipole interaction mechanism. Steric hindrance exerted by other moieties can help modulating the interactions and tuning the energy transfer process. Overall, considering also the relatively greater importance of intra-molecular nuclear motions, the protein environment around biological chromophores does not appear fine-tuned for a specific function.

How and How Much Molecular Conformation Affects Electronic Circular Dichroism: The Case of 1,1-Diarylcarbinols.

Chiroptical spectra such as electronic circular dichroism (ECD) are said to be much more sensitive to conformation than their non-chiroptical counterparts, however, it is difficult to demonstrate such a common notion in a clear-cut way. We run DFT and TDDFT calculations on two closely related 1,1-diarylmethanols which show mirror-image ECD spectra for the same absolute configuration. We demonstrate that the main reason for the different chiroptical response of the two compounds lies in different conformational ensembles, caused by a single hydrogen-to-methyl substitution. We conclude that two compounds, having the same configuration but different conformation, may exhibit mirror-image ECD signals, stressing the importance and impact of conformational factors on ECD spectra.

The shape of the electronic circular dichroism spectrum of (2,6-dimethylphenyl)(phenyl)methanol: interplay between conformational equilibria and vibronic effects.

Comparison between chiroptical spectra and theoretical predictions is the method of choice for the assignment of the absolute configuration of chiral compounds in solution. Here we report the case of an apparently simple biarylcarbinol, whose electronic circular dichroism (ECD) in the 1Lb region exhibits a peculiar alternation of negative and positive bands. Adopting Density Functional Theory, and describing solvent effects with implicit methods, we found three stable conformers in ethanol, each of them with two close lying states corresponding to similar local 1Lb excitations on the two phenyls. We computed the corresponding vibronic ECD spectra in harmonic approximation, including Duschinsky mixings as well as both Franck Condon (FC) and Herzberg Teller (HT) effects. Exploiting a recently developed mixed quantum/classical method, we further investigated the contribution of the vibronic spectra of out-of-equilibrium structures along the interconversion path connecting the different conformers. In this way, we achieved a reasonable agreement with experiment and attributed the alternating signs of the bands to the existence of different conformers. The remaining discrepancies with experiment indicate that specific solute-solvent interactions modulate the relative conformers' stabilities, calling for new methods able to combine Molecular Dynamics explorations and vibronic calculations. Moreover, the poor performance of HT approaches and the existence of two closely-lying states suggest the necessity of an improved fully-nonadiabatic vibronic approach. These findings demonstrate that even for such a simple system as the biarylcarbinol investigated here, a full reproduction of the fine details of the ECD spectrum requires the development of new improved methods.

Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum.

We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.

The "Case of Two Compounds with Similar Configuration but Nearly Mirror Image CD Spectra" Refuted. Reassignment of the Absolute Configuration of N-Formyl-3',4'-dihydrospiro[indan-1,2'(1'H)-pyridine].

In 1997, Sandström and co-workers reported the case of two chiral spiro compounds with very similar skeletons but showing almost mirror-image electronic circular dichroism (ECD) spectra for the corresponding absolute configuration. The paper has been often cited as a proof and good educational example of the pronounced sensitivity of ECD toward molecular conformation, and a clear warning against the use of ECD spectral correlations to assign absolute configurations. Although both concepts remain valid, they are not exemplified by the quoted paper. We demonstrate that the original configurational assignment of one compound was wrong and revise it by using TDDFT calculations. The main reason for the observed failure is the use of the matrix method, a popular approach to predict ECD spectra of compounds which can be treated with an independent system approximation (ISA), including proteins. Using a modern version of the matrix method, we demonstrate that the ISA is not valid for the title compound. Even in the absence of apparent conjugation between the component chromophores, the validity of the ISA should never be taken for granted and the effective extent of orbital overlap should always be verified.

Synthesis, X-ray, and Spectroscopic Study of Dissymmetric Tetrahedral Zinc(II) Complexes from Chiral Schiff Base Naphthaldiminate Ligands with Apparent Exception to the ECD Exciton Chirality.

Bidentate enantiopure Schiff base ligands, (R or S)-N-1-(Ar)ethyl-2-oxo-1-naphthaldiminate (R- or S-N^O), diastereoselectively provide Λ- or Δ-chiral-at-metal four-coordinated Zn(R- or S-N^O)2 {Ar = C6H5; Zn-1R or Zn-1S and p-C6H4OMe; Zn-2R or Zn-2S}. Two R- or S-N^O-chelate ligands coordinate to the zinc(II) in a tetrahedral mode and induce Λ- or Δ-configuration at the zinc metal center. In the solid state, the R- or S-ligand diastereoselectively gives Λ- or Δ-Zn configuration, respectively, and forms enantiopure crystals. Single crystal structure determinations show two symmetry-independent molecules (A and B) in each asymmetric unit to give Z' = 2 structures. Electronic circular dichroism (ECD) spectra show the expected mirror image relationship resulting from diastereomeric excess toward the Λ-Zn for R-ligands and Δ-Zn for S-ligands in solution. ECD spectra are well reproduced by TDDFT calculations, while the application of the exciton chirality method, in the common point-dipole approximation, predicts the wrong sign for the long-wavelength couplet. A dynamic diastereomeric equilibrium (Λ vs Δ) prevails for both R- and S-ligand-metal complexes in solution, respectively, evidenced by (1)H NMR spectroscopy. Variable temperature (1)H NMR spectra show a temperature-dependent shift of the diastereomeric equilibrium and confirm Δ-Zn configuration (for S-ligand) to be the most stable one and favored at low temperature. DSC analyses provide quantitative diastereomeric excess in the solid state for Zn-2R and Zn-2S, which is comparable to the results of solution studies.

A Combined Experimental-Computational Investigation to Uncover the Puzzling (Chiro-)optical Response of Pyridocyclophanes: One- and Two-Photon Spectra.

A combined experimental-computational analysis of the one- and two-photon absorption (OPA, TPA) and the electronic circular dichroism (ECD) of complex chiral shape-persistent (2,6)-pyrido[142 ]allenoacetylenic cyclophane, (P,P,P,P)-MC[142 ] enantiomers, sheds light on the origin of their peculiar spectral signatures. The study on MC[142 ], which is represented in solution by three possible conformers, indicates that two of them (chair and twist) are the prevalent conformers at room temperature; the population ratio depending on the solvent. The complex shape of the red-edge of the UV and ECD spectra is qualitatively reproduced by using vibronic calculations and assigned to progressions on the ethynyl stretchings observable only in the chair and twist conformers. The picture arising from the analysis of the linear spectra is confirmed by two-photon spectroscopies, showing that they constitute valuable tools for the exploration of high-energy electronic transitions in pyridoallenoacetylenic cyclophanes. Discrepancies among computed and experimental spectra point out that an accurate description of such complex systems with a large delocalized π framework and a dense manifold of electronic excited state remains a challenge for theoretical models.

Improved hemicryptophane hosts for the stereoselective recognition of glucopyranosides.

Four new enantiomerically and diastereomerically pure hemicryptophane hosts (M-SSS-2/P-SSS-2 and M-RRR-2/P-RRR-2 pairs) were designed for the recognition of sugar derivatives. Their absolute configuration was determined from the circular dichroism spectra and DFT calculations. The host molecules were then used for the stereoselective recognition of glucopyranosides. Binding constants were obtained from (1)H NMR titration experiments showing an increase of affinity for this class of receptors, associated with an improved diastereo- and enantio-differentiation.

Magnetic circular dichroism of porphyrin lanthanide M3+ complexes.

Lanthanide complexes exhibit interesting spectroscopic properties yielding many applications as imaging probes, natural chirality amplifiers, and therapeutic agents. However, many properties are not fully understood yet. Therefore, we applied magnetic circular dichroism (MCD) spectroscopy, which provides enhanced information about the underlying electronic structure to a series of lanthanide compounds. The metals in the M(3+) state included Y, La, Eu, Tb, Dy, Ho, Er, Tm, Yb, and Lu; the spectra were collected for selected tetraphenylporphin (TPP) and octaethylporphin (OEP) complexes in chloroform. While the MCD and UV-VIS absorption spectra were dominated by the porphyrin signal, metal binding significantly modulated them. MCD spectroscopy was found to be better suited to discriminate between various species than absorption spectroscopy alone. The main features and trends in the lanthanide series observed in MCD and absorption spectra of the complexes could be interpreted at the Density Functional Theory (DFT) level, with effective core potentials on metal nuclei. The sum over state (SOS) method was used for simulation of the MCD intensities. The combination of the spectroscopy and quantum-chemical computations is important for understanding the interactions of the metals with the organic compounds.

Strong intermolecular exciton couplings in solid-state circular dichroism of aryl benzyl sulfoxides.

A series of 13 enantiopure aryl benzyl sulfoxides () with different substituents on the two aromatic rings has been previously analyzed by means of electronic circular dichroism (CD) spectroscopy. Most of these compounds are crystalline and their X-ray structure is established. For almost one-half of the series, CD spectra measured in the solid state were quite different from those in acetonitrile solution. We demonstrate that the difference is due to strong exciton couplings between molecules packed closely together in the crystal. The computational approach consists of time-dependent density functional theory (TDDFT) calculations run on "dimers" composed of nearest neighbors found in the lattice. Solid-state CD spectra are well reproduced by the average of all possible pairwise terms. The relation between the crystal space group and conformation, and the appearance of solid-state CD spectra, is also discussed.

Discriminating Clockwise and Counterclockwise Photoisomerization Paths in Achiral Photoswitches by Excited-State Electronic Circular Dichroism.

Despite the numerous investigations of photoisomerization reactions from both the computational and experimental points of view, even in complex environments, to date there is no direct demonstration of the direction of rotation of the retinal chromophore, initiating the vision process in several organisms, occurring upon light irradiation. In the literature, many proposals have been formulated to shed light on the details of this process, most of which are extracted from semiclassical simulations. Although high hopes are held in the development of time-resolved X-ray spectroscopy, I argue in this work that simpler but less known techniques can be used to unravel the details of this fascinating photochemical process. In fact, chiroptical spectroscopy would unambiguously prove the direction of the rotatory motion of the chromophore during the photoisomerization process by probing excited state chirality, a piece of information that, so far, has been exclusively extracted from atomistic simulations. I demonstrate this statement by computing the expected chiroptical response along photoisomerization pathways for several models of the retinal chromophores that are found in nature bound to rhodopsins, including nuclear ensemble spectra from semiclassical dynamics simulations, that can be compared with time-resolved experiments.

A Computational Perspective on the Reactivity of π-spacers in Self-Immolative Elimination Reactions.

The controlled release of chemicals, especially in drug delivery, is crucial, often employing "self-immolative" spacers to enhance reliability. These spacers separate the payload from the protecting group, ensuring a more controlled release. Over the years, design rules have been proposed to improve the elimination process's reaction rate by modifying spacers with electron-donating groups or reducing their aromaticity. The spacer design is critical for determining the range of functional groups released during this process. This study explores various strategies from the literature aimed at improving release rates, focusing on the electronic nature of the spacer, its aromaticity, the electronic nature of its substituents, and the leaving groups involved in the elimination reaction. Through computational analysis, I investigate activation free energies by identifying transition states for model reactions. My calculations align qualitatively with experimental results, demonstrating the feasibility and reliability of computationally pre-screening model self-immolative eliminations. This approach allows proposing optimal combinations of spacer and leaving group for achieving the highest possible release rate.

A novel bioresponsive self-immolative spacer based on aza-quinone methide reactivity for the controlled release of thiols, phenols, amines, sulfonamides or amides.

A stimuli-sensitive linker is one of the indispensable components of prodrugs for cancer therapy as it covalently binds the drug and releases it upon external stimulation at the tumour site. Quinone methide elimination has been widely used as the key transformation to release drugs based on their nucleofugacity. The usual approach is to bind the drug to the linker as a carbamate and release it as a free amine after a self-immolative 1,6-elimination. Although this approach is very efficient, it is limited to amines (as carbamates), alcohols or phenols (as carbonates) or other acidic functional groups. We report here a self-immolative spacer capable of directly linking and releasing amines, phenols, thiols, sulfonamides and carboxyamides after a reductive stimulus. The spacer is based on the structure of (5-nitro-2-pyrrolyl)methanol (NPYM-OH), which was used for the direct alkylation of the functional groups mentioned above. The spacer is metabolically stable and has three indispensable sites for bioconjugation: the bioresponsive trigger, the conjugated 1,6 self-immolative system and a third arm suitable for conjugation with a carrier or other modifiers. Release was achieved by selective reduction of the nitro group over Fe/Pd nanoparticles (NPs) in a micellar aqueous environment (H2O/TPGS-750-M), or by NADH mediated nitroreductase activation. A DFT study demonstrates that, during the 1,6 elimination, the transition state formed from 5-aminopyrrole has a lower activation energy compared to other 5-membered heterocycles or p-aminobenzyl derivatives. The NPYM scaffold was validated by late-stage functionalisation of approved drugs such as celecoxib, colchicine, vorinostat or ciprofloxacin. A hypoxia-activated NPYM-based prodrug (HAP) derived from HDAC inhibitor ST7612AA1 was also produced, which was active in cancer cells under hypoxic conditions.

Intermolecular exciton coupling and vibronic effects in solid-state circular dichroism: a case study.

The electronic circular dichroism (CD) spectrum of the sesquiterpenoid 1ß,10ß-epoxydesacetoxymatricarin (1) measured in the microcrystalline solid state differs from the solution one in the appearance of a pronounced vibrational fine structure in the long-wavelength region (n-π* enone transition) and of a new moderately intense band in the π-π* region. TDDFT CD calculations were run on input structures derived from the X-ray geometry of 1 to reproduce the impact of exciton-type couplings between proximate molecules in the crystals. The vibrational structure of the CD spectrum was also reproduced for the isolated molecule by modelling the potential energy surfaces at the harmonic level and taking into account Duschinsky and Herzberg-Teller effects.