Psi4 is a free and open-source ab initio electronic structure program providing Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of Psi4's core functionality via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSchema data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCArchive Infrastructure project, make the latest version of Psi4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs. File list (2) download file view on ChemRxiv psi4.pdf (4.37 MiB) download file view on ChemRxiv supplementary_material.pdf (297.86 KiB)

Tetracoordinated phosphorus atoms in derivatives of cyclophosphazenes are pentavalent and are potentially chiral. Chirality does not seem to have been investigated nor discussed for any literature examples of crystal structures of those cyclophosphazene compounds which are expected to be chiral. In cyclotriphosphazatriene compounds with ansa-substituted macrocyclic rings the two phosphorus atoms attached to the macrocycle are chiral, although the cis-ansa cyclotriphosphazatriene-macrocycle 1 is the meso form. Reaction of 1 with the di-secondary amine, piperazine, provides a convenient way to investigate the chiral configurational properties of cyclophosphazene compounds. It is found by X-ray crystallography that there are two configurational isomers (one meso and one racemate) of the singly bridged di(cyclophosphazene-macrocyclic) piperazine derivative 6i, and that there are two configurational isomers (both meso) of the doubly bridged di(cyclophosphazene-macrocyclic) piperazine derivative 8i; in 8i one meso form has a center of symmetry and the other a plane of symmetry. The chiral configurational properties of each stage of the reaction scheme for formation of 6i and 8i from 1 have been confirmed by 31 P NMR spectroscopy and the results are consistent with inversion of configuration at phosphorus at each step of the reaction of >P(OR)Cl groups with HNR′R′′ to form >P(OR)(NR′R′′) derivatives: viz. reaction of 1 with piperazine gives the monosubstituted compound 4i, which exists as a racemate with the macrocyclic ring in the trans-configuration; reaction of compound 4i with 1 gives the two configurational forms (meso and racemate) of the singly bridged derivative 6i with the macrocyclic rings in the trans-trans configuration; reaction of 6i with piperazine gives the monosubstituted singly bridged derivative 7i, which exists as two racemic mixtures with the macrocyclic rings in cis-trans configurations; and intramolecular condensation of 7i gives the two configurational forms of the doubly bridged derivative 8i with each of the macrocyclic rings in the cis-cis configuration. In this work the configurational properties of derivatives of cyclotriphosphazatriene rings with two (one N 3 P 3 unit) or four (two N 3 P 3 units) chiral centers have been rationalized. It is found that the chiral structures of cyclotriphosphazatriene derivatives may be represented by 2D molecular diagrams, as long as the Fischer rules for chiral carbon compounds are followed for phosphorus compounds.

Background: Genetic variants of high temperature requirement factor A1 (HTRA1) associate with AMD risk. Results: Growth differentiation factor 6 (GDF6) gene polymorphism significantly associated with AMD. HTRA1 knock-out mice display reduced blood vessel in retina and up-regulation of GDF6. Conclusion: HTRA1 regulates angiogenesis via TGF-␤ signaling by GDF6, a novel disease gene. Significance: This novel pathway of HTRA1 in regulation of vascularization is critical for understanding AMD pathogenesis.

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Here, we present a concise model which can predict the photoluminescent properties of a given compound from first principles, both within and beyond the Franck-Condon approximation. The formalism required to compute fluorescence, Internal Conversion (IC), and Inter-System Crossing (ISC) is discussed. The IC mechanism in particular is a difficult pathway to compute due to difficulties associated with the computation of required bosonic configurations and non-adiabatic coupling elements. Here, we offer a discussion and breakdown on how to model these pathways at the Density Functional Theory (DFT) level, with respect to its computational implementation, strengths and current limitations. The model is then used to compute the photoluminescent quantum yield (PLQY) of a number of small but important compounds: Anthracene, Tetracene, Pentacene, diketo-pyrrolo-pyrrole (DPP), and Perylene Diimide (PDI), within a polarizable continuum model. Rate constants for fluorescence, IC, and ISC compare well for the most part with respect to experiment, despite triplet energies being overestimated to a degree. The resulting PLQYs are promising with respect to the level of theory being DFT. While we obtained a positive result for PDI within the Franck-Condon limit, the other systems require a second order correction. Recomputing quantum yields with Herzberg-Teller terms yields PLQYs of 0.19, 0.08, 0.04, 0.70, and 0.99 for Anthracene, Tetracene, Pentacene, DPP, and PDI respectively. Based on these results, we are confident the presented methodology is sound with respect to the level of quantum chemistry, and presents an important stepping stone in the search for a tool to predict properties of larger, coupled systems.

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<div> <div> <div> <p>Psi4 is a free and open-source ab initio electronic structure program providing Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of Psi4’s core functionality via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSchema data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCArchive Infrastructure project, make the latest version of Psi4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs. </p> </div> </div> </div>