Abstract:Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PyAdf, a scripting framework for quantum chemistry. PyAdf handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object-oriented implementation in the Python programming language. We give an overview of the capabilities of PyAdf and illustrate its usefulness in quantum-chemical multiscale simulations with a number of examples taken from recent applications.
The first intermediate of the photochemical transformation of ortho-nitrobenzaldehyde to ortho-nitrosobenzoic acid in acetonitrile solvent has been characterized by femtosecond spectroscopy and time-dependent density functional theory (TDDFT) calculations. Femtosecond stimulated Raman spectroscopy (FSRS) indicates that this intermediate adopts a ketene structure. This assignment is supported by the TDDFT results. A kinetic analysis of FSRS and transient absorption data points to two channels for the formation of the ketene. For the predominating first channel the formation takes 0.4 ps. For the second channel it is much slower and takes 220 ps. We assign the first channel to a reaction via an excited singlet state. The second one might involve a triplet state.
The ability to calculate accurate electron densities of full proteins or of selected sites in proteins is a prerequisite for a fully quantum-mechanical calculation of protein-protein and protein-ligand interaction energies. Quantum-chemical subsystem methods capable of treating proteins and other biomolecular systems provide a route to calculate the electron densities of proteins efficiently and further make it possible to focus on specific parts. Here, we evaluate and extend the 3-partition frozen-density embedding (3-FDE) scheme [Jacob, C. R.; Visscher, L. J. Chem. Phys.2008, 128, 155102] for this purpose. In particular, we have extended this scheme to allow for the treatment of disulfide bridges and charged amino acid residues and have introduced the possibility to employ more general partitioning schemes. These extensions are tested both for the prediction of full protein electron densities and for focusing on the electron densities of a selected protein site. Our results demonstrate that 3-FDE is a promising tool for the fully quantum-chemical treatment of proteins.
We present the software package MOVIPAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MOVIPAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add-ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta-program design, MOVIPAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode-and Intensity-Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large p-helix consisting of 20 (S)-alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of aand 3 10 -helical analogs.
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