QC Lab is an open-source Python package for quantum–classical (QC) dynamics simulations aimed to promote the development of QC algorithms, and their application to a wide variety of relevant model problems. It follows a modular design that facilitates cross-compatibility between algorithms and models. By decomposing algorithms and models into a series of tasks and ingredients that can be substituted and reused, it minimizes development efforts and code redundancy. In this Paper, we introduce the first stable version of QC Lab, and describe its design philosophy.

We discuss the computation of partial Auger decay widths with equation-of-motion ionization-potential coupled-cluster (EOMIP-CCSD) theory in the framework of non-Hermitian quantum mechanics (NHQM). In NHQM, the decaying character of metastable states is described with complex energies and the total decay width is obtained directly from the total energy. In contrast, the computation of partial decay widths, i.e., the contributions of different decay channels to the total width, requires further analysis. However, partial widths are important for Auger spectroscopy as they determine the probability with which different final states are formed and hence the shape of the Auger spectrum. Recently, we introduced Auger channel projectors (ACPs), which selectively remove decay channels from the EOMIP-CCSD excitation manifold. This method requires a separate EOMIP-CCSD calculation for each decay channel. Here, we suggest an alternative: We solve the EOMIP-CCSD equations for the core-ionized state in the full excitation manifold and decompose the imaginary part of the resulting energy. In this way, we obtain all partial decay widths at once. We compute Auger spectra for K-edge-ionized states of methane, ethane, and hydrogen sulfide, and a Coster–Kronig spectrum for L1-edge-ionized hydrogen sulfide. The results obtained with our new approach differ only negligibly from ACP results. We also present the first Auger spectra for the cyanide anion, including vibrational broadening, and discuss the differences between the spectra of the carbon core hole and the nitrogen core hole.

The N-benzyloxycarbonyl-l-alanine molecule is a derivative of the l-α-alanine amino acid with a benzyl carbamate protecting group at the N-terminus, more commonly denoted Cbz-Ala or Z-Ala. In this computational investigation, we sought to determine the available isomers of Z-Ala and their distinguishing spectroscopic signatures via quantum-chemistry methods. Sixty-five total isomers were obtained, and coupled-cluster- and perturbation-theory-based relative energies were computed. The two nearly degenerate, lowest-energy isomers were found to differ in their configuration than the lowest-energy form of isolated alanine, suggesting that the protecting group changes the dominant form of Ala. Through comparisons to exhaustive sampling of Ala and benzyl formate isomers, nearly all of the Z-Ala structures could be ascribed to fragment-paired structural motifs, with a few outliers exhibiting new intramolecular interactions between the constituent fragments. Based on this observation, an assessment of the additivity of the two fragments’ relative energies was performed for Z-Ala energies. Many of the isomers’ energies were reasonably described by such considerations, although backbone strain and hydrogen-bonding interactions altered this energy landscape and led to nonadditive effects for several of the isomers. Comparison to experimental REMPI-based UV/IR ion-dip vibrational spectra in the 90–1822 cm–1 region indicated that two isomers are dominantly present at the experimental conditions, although signatures of other isomers from the ensemble were also observed. Clear assignments of structural motifs were possible through this experimental comparison. Computed coupled-cluster benchmarks allowed for methodology assessments in this study. The modified opposite-spin MP2 method (MOS-RI-MP2) was found to be particularly accurate, relative to these benchmarks, after minor adjustment of the range-separation parameter. Density functional theory (DFT) methods were found to be variable in their accuracy for both energies and spectra, although a few key functionals performed particularly well for this system in the low-frequency region of the vibrational spectrum. These methodology constraints provided recommendations for similar systems and subsequent anharmonic analyses.

Transition state modeling is a powerful tool for unraveling the mechanistic intricacies of chemical reactions. It plays a pivotal role in the design of innovative catalytic systems, facilitating progress in the field of catalysis. A carbon-neutral chemical hydrogen battery is the most relevant approach for the storage and transportation of hydrogen fuel. Herein, with the aid of transition state models, we decipher the mode of activity of the pincer-ligated manganese complex that enables the reversible hydrogenation and dehydrogenation process for the efficient H2 storage and release. We identified the critical contributions from the basic amino acids, specifically lysine and its potassium salt, as well as the influence of solvent, counterions, and water, in governing the reversibility. In addition, we have probed into the role of noncovalent interactions during the capture and release of CO2 by potassium lysinate, thereby enabling the realization of a carbon-neutral chemical hydrogen battery system.