Selected Columns of the Density Matrix in an Atomic Orbital Basis I: An Intrinsic and Non-iterative Orbital Localization Scheme for the Occupied Space.

In this work, we extend the selected columns of the density matrix (SCDM) methodology [J. Chem. Theory Comput. 2015, 11, 1463-1469]─a non-iterative and real-space procedure for generating localized occupied orbitals for condensed-phase systems─to the construction of local molecular orbitals (LMOs) in systems described using non-orthogonal atomic orbital (AO) basis sets. In particular, we introduce three different theoretical and algorithmic variants of SCDM (referred to as SCDM-M, SCDM-L, and SCDM-G) that can be used in conjunction with the AO basis sets used in standard quantum chemistry codebases. The SCDM-M and SCDM-L variants are based on a pivoted QR factorization of the Mulliken and Löwdin representations of the density matrix and are tantamount to selecting a well-conditioned set of projected atomic orbitals (PAOs) and projected (symmetrically-) orthogonalized atomic orbitals, respectively, as proto-LMOs that can be orthogonalized to exactly span the occupied space. The SCDM-G variant is based on a real-space (grid) representation of the wavefunction, and therefore has the added flexibility of considering a large number of grid points (or δ functions) when selecting a set of well-conditioned proto-LMOs. A detailed comparative analysis across molecular systems of varying size, dimensionality, and saturation level reveals that the LMOs generated by these three non-iterative/direct SCDM variants are robust, comparable in orbital locality to those produced with the iterative Boys or Pipek-Mezey (PM) localization schemes, and completely agnostic toward any single orbital locality metric. Although all three SCDM variants are based on the density matrix, we find that the character of the generated LMOs can differ significantly between SCDM-M, SCDM-L, and SCDM-G. In this regard, only the grid-based SCDM-G procedure (like PM) generates LMOs that qualitatively preserve σ-π symmetry (in systems such as s-trans alkenes), and are well-aligned with chemical (i.e., Lewis structure) intuition. While the direct and standalone use of SCDM-generated LMOs should suffice for most chemical applications, our findings also suggest that the use of these orbitals as an unbiased and cost-effective (initial) guess also has the potential to improve the convergence of iterative orbital localization schemes, in particular for large-scale and/or pathological molecular systems.

ColabFit exchange: Open-access datasets for data-driven interatomic potentials.

Data-driven interatomic potentials (IPs) trained on large collections of first principles calculations are rapidly becoming essential tools in the fields of computational materials science and chemistry for performing atomic-scale simulations. Despite this, apart from a few notable exceptions, there is a distinct lack of well-organized, public datasets in common formats available for use with IP development. This deficiency precludes the research community from implementing widespread benchmarking, which is essential for gaining insight into model performance and transferability, and also limits the development of more general, or even universal, IPs. To address this issue, we introduce the ColabFit Exchange, the first database providing open access to a large collection of systematically organized datasets from multiple domains that is especially designed for IP development. The ColabFit Exchange is publicly available at https://colabfit.org, providing a web-based interface for exploring, downloading, and contributing datasets. Composed of data collected from the literature or provided by community researchers, the ColabFit Exchange currently (September 2023) consists of 139 datasets spanning nearly 70 000 unique chemistries, and is intended to continuously grow. In addition to outlining the software framework used for constructing and accessing the ColabFit Exchange, we also provide analyses of the data, quantifying the diversity of the database and proposing metrics for assessing the relative diversity of multiple datasets. Finally, we demonstrate an end-to-end IP development pipeline, utilizing datasets from the ColabFit Exchange, fitting tools from the KLIFF software package, and validation tests provided by the OpenKIM framework.

Artificial intelligence assisted whole organ pancreatic fat estimation on magnetic resonance imaging and correlation with pancreas attenuation on computed tomography.

BACKGROUND: Fatty pancreas is associated with inflammatory and neoplastic pancreatic diseases. Magnetic resonance imaging (MRI) is the diagnostic modality of choice for measuring pancreatic fat. Measurements typically use regions of interest limited by sampling and variability. We have previously described an artificial intelligence (AI)-aided approach for whole pancreas fat estimation on computed tomography (CT). In this study, we aimed to assess the correlation between whole pancreas MRI proton-density fat fraction (MR-PDFF) and CT attenuation. METHODS: We identified patients without pancreatic disease who underwent both MRI and CT between January 1, 2015 and June 1, 2020. 158 paired MRI and CT scans were available for pancreas segmentation using an iteratively trained convolutional neural network (CNN) with manual correction. Boxplots were generated to visualize slice-by-slice variability in 2D-axial slice MR-PDFF. Correlation between whole pancreas MR-PDFF and age, BMI, hepatic fat and pancreas CT-Hounsfield Unit (CT-HU) was assessed. RESULTS: Mean pancreatic MR-PDFF showed a strong inverse correlation (Spearman -0.755) with mean CT-HU. MR-PDFF was higher in males (25.22 vs 20.87; p = 0.0015) and in subjects with diabetes mellitus (25.95 vs 22.17; p = 0.0324), and was positively correlated with age and BMI. The pancreatic 2D-axial slice-to-slice MR-PDFF variability increased with increasing mean whole pancreas MR-PDFF (Spearman 0.51; p < 0.0001). CONCLUSION: Our study demonstrates a strong inverse correlation between whole pancreas MR-PDFF and CT-HU, indicating that both imaging modalities can be used to assess pancreatic fat. 2D-axial pancreas MR-PDFF is variable across slices, underscoring the need for AI-aided whole-organ measurements for objective and reproducible estimation of pancreatic fat.

Inverse molecular design from first principles: Tailoring organic chromophore spectra for optoelectronic applications.

The discovery of molecules with tailored optoelectronic properties, such as specific frequency and intensity of absorption or emission, is a major challenge in creating next-generation organic light-emitting diodes (OLEDs) and photovoltaics. This raises the following question: How can we predict a potential chemical structure from these properties? Approaches that attempt to tackle this inverse design problem include virtual screening, active machine learning, and genetic algorithms. However, these approaches rely on a molecular database or many electronic structure calculations, and significant computational savings could be achieved if there was prior knowledge of (i) whether the optoelectronic properties of a parent molecule could easily be improved and (ii) what morphing operations on a parent molecule could improve these properties. In this Perspective, we address both of these challenges from first principles. We first adapt the Thomas-Reiche-Kuhn sum rule to organic chromophores and show how this indicates how easily the absorption and emission of a molecule can be improved. We then show how by combining electronic structure theory and intensity borrowing perturbation theory we can predict whether or not the proposed morphing operations will achieve the desired spectral alteration, and thereby derive widely applicable design rules. We go on to provide proof-of-concept illustrations of this approach to optimizing the visible absorption of acenes and the emission of radical OLEDs. We believe that this approach can be integrated into genetic algorithms by biasing morphing operations in favor of those that are likely to be successful, leading to faster molecular discovery and greener chemistry.

Switching between Coherent and Incoherent Singlet Fission via Solvent-Induced Symmetry Breaking.

Singlet fission in organic semiconductors causes a singlet exciton to decay into a pair of triplet excitons and holds potential for increasing the efficiency of photovoltaic devices. In this combined experimental and theoretical study, we reveal that a covalent dimer of the organic semiconductor tetracene undergoes activated singlet fission by qualitatively different mechanisms depending on the solvent environment. We show that intramolecular vibrations are an integral part of this mechanism, giving rise to mixing between charge transfer and triplet pair excitations. Either coherent or incoherent singlet fission can occur, depending on the transient solvent-induced energetic proximity between the states, giving rise to complex variation of the singlet fission mechanism and time scale in the different environments. Our results suggest a more general principle for controlling the efficiency of photochemical reactions by utilizing transient interactions to tune the energetics of reactant and product states and switch between incoherent and coherent dynamics.

Anticipating Acene-Based Chromophore Spectra with Molecular Orbital Arguments.

Recent synthetic studies on the organic molecules tetracene and pentacene have found certain dimers and oligomers to exhibit an intense absorption in the visible region of the spectrum that is not present in the monomer or many previously studied dimers. In this article we combine experimental synthesis with electronic structure theory and spectral computation to show that this absorption arises from an otherwise dark charge-transfer excitation "borrowing intensity" from an intense UV excitation. Further, by characterizing the role of relevant monomer molecular orbitals, we arrive at a design principle that allows us to predict the presence or absence of an additional absorption based on the bonding geometry of the dimer. We find this rule correctly explains the spectra of a wide range of acene derivatives and solves an unexplained structure-spectrum phenomenon first observed over 70 years ago. These results pave the way for the design of highly absorbent chromophores with applications ranging from photovoltaics to liquid crystals.

Tuning Singlet Fission in π-Bridge-π Chromophores.

We have designed a series of pentacene dimers separated by homoconjugated or nonconjugated bridges that exhibit fast and efficient intramolecular singlet exciton fission (iSF). These materials are distinctive among reported iSF compounds because they exist in the unexplored regime of close spatial proximity but weak electronic coupling between the singlet exciton and triplet pair states. Using transient absorption spectroscopy to investigate photophysics in these molecules, we find that homoconjugated dimers display desirable excited-state dynamics, with significantly reduced recombination rates as compared to conjugated dimers with similar singlet fission rates. In addition, unlike conjugated dimers, the time constants for singlet fission are relatively insensitive to the interplanar angle between chromophores, since rotation about σ bonds negligibly affects the orbital overlap within the π-bonding network. In the nonconjugated dimer, where the iSF occurs with a time constant >10 ns, comparable to the fluorescence lifetime, we used electron spin resonance spectroscopy to unequivocally establish the formation of triplet-triplet multiexcitons and uncoupled triplet excitons through singlet fission. Together, these studies enable us to articulate the role of the conjugation motif in iSF.

A Direct Mechanism of Ultrafast Intramolecular Singlet Fission in Pentacene Dimers.

Interest in materials that undergo singlet fission (SF) has been catalyzed by the potential to exceed the Shockley-Queisser limit of solar power conversion efficiency. In conventional materials, the mechanism of SF is an intermolecular process (xSF), which is mediated by charge transfer (CT) states and depends sensitively on crystal packing or molecular collisions. In contrast, recently reported covalently coupled pentacenes yield ∼2 triplets per photon absorbed in individual molecules: the hallmark of intramolecular singlet fission (iSF). However, the mechanism of iSF is unclear. Here, using multireference electronic structure calculations and transient absorption spectroscopy, we establish that iSF can occur via a direct coupling mechanism that is independent of CT states. We show that a near-degeneracy in electronic state energies induced by vibronic coupling to intramolecular modes of the covalent dimer allows for strong mixing between the correlated triplet pair state and the local excitonic state, despite weak direct coupling.