We present the GMTKN55 benchmark database for general main group thermochemistry, kinetics and noncovalent interactions. Compared to its popular predecessor GMTKN30 [Goerigk and Grimme J. Chem. Theory Comput., 2011, 7, 291], it allows assessment across a larger variety of chemical problems-with 13 new benchmark sets being presented for the first time-and it also provides reference values of significantly higher quality for most sets. GMTKN55 comprises 1505 relative energies based on 2462 single-point calculations and it is accessible to the user community via a dedicated website. Herein, we demonstrate the importance of better reference values, and we re-emphasise the need for London-dispersion corrections in density functional theory (DFT) treatments of thermochemical problems, including Minnesota methods. We assessed 217 variations of dispersion-corrected and -uncorrected density functional approximations, and carried out a detailed analysis of 83 of them to identify robust and reliable approaches. Double-hybrid functionals are the most reliable approaches for thermochemistry and noncovalent interactions, and they should be used whenever technically feasible. These are, in particular, DSD-BLYP-D3(BJ), DSD-PBEP86-D3(BJ), and B2GPPLYP-D3(BJ). The best hybrids are ωB97X-V, M052X-D3(0), and ωB97X-D3, but we also recommend PW6B95-D3(BJ) as the best conventional global hybrid. At the meta-generalised-gradient (meta-GGA) level, the SCAN-D3(BJ) method can be recommended. Other meta-GGAs are outperformed by the GGA functionals revPBE-D3(BJ), B97-D3(BJ), and OLYP-D3(BJ). We note that many popular methods, such as B3LYP, are not part of our recommendations. In fact, with our results we hope to inspire a change in the user community's perception of common DFT methods. We also encourage method developers to use GMTKN55 for cross-validation studies of new methodologies.

The implementation of a novel tight-binding Hamiltonian within the QCEIMS program allows the first-principles based computation of EI mass spectra within a few hours for systems containing elements up to Z = 86.

The fractional occupation number weighted density (FOD) analysis is explored as a general theoretical diagnostic for complicated electronic structures. Its main feature is to provide robustly and quickly the information on the localization of "hot" (strongly correlated and chemically active) electrons in a molecule. We demonstrate its usage in four different prototypical applications: 1) As a new and fast measure of the biradical character of polycyclic aromatic hydrocarbons, 2) for the selection of active orbital spaces in multiconfigurational or complete active space self consistent field (MCSCF/CASSCF) treatments, 3) as a possibility to describe molecular-energy landscapes consistently in regions with varying biradical character, as exemplified by partial double-bond torsions, and 4) as a powerful visualization method for static electron correlation effects in large biomolecules in connection with an efficient semi-empirical tight-binding molecular orbital scheme. The last application opens a full quantum-mechanical, unbiased route to the automatic detection of errors in experimental protein X-ray structures, such as false protonation states or misplaced atoms. In the first example, the complete (unfragmented) quantum-chemical calculation of the FOD for an entire metalloprotein with more than 7500 atoms is described.

The prediction of electron ionization (EI) mass spectra (MS) from first principles has been a major challenge for quantum chemistry (QC). The unimolecular reaction space grows rapidly with increasing molecular size. On the one hand, statistical models like Eyring's quasi-equilibrium theory and Rice-Ramsperger-Kassel-Marcus theory have provided valuable insight, and some predictions and quantitative results can be obtained from such calculations. On the other hand, molecular dynamics-based methods are able to explore automatically the energetically available regions of phase space and thus yield reaction paths in an unbiased way. We describe in this feature article the status of both methodologies in relation to mass spectrometry for small to medium sized molecules. We further present results obtained with the QCEIMS program developed in our laboratory. Our method, which incorporates stochastic and dynamic elements, has been a significant step toward the reliable routine calculation of EI mass spectra.

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We present an automated quantum chemical protocol for the determination of preferred protonation sites in organic and organometallic molecules containing up to a few hundred atoms. It is based on the Foster-Boys orbital localization method, whereby we automatically identify lone pairs and π orbitals as possible protonation sites. The method becomes efficient in conjunction with the robust and fast GFN-xTB semiempirical method proposed recently (Grimme et al., J. Chem. Theory Comput. 2017, 13, 1989). The protonated isomers that are found within a few seconds to minutes of computational wall-time on a standard desktop computer are then energetically refined using density functional theory (DFT), where we use a high-level double-hybrid reference method to benchmark GFN-xTB and low-cost DFT approaches. The proposed DFT/GFN-xTB/LMO composite protocol is generally applicable to almost arbitrary molecules including transition metal complexes. Importantly it is found that even in electronically complicated cases, the GFN-xTB optimized protomer structures are reasonable and can safely be used in single-point DFT calculations. Corrections from energy to free energy mostly have a small effect on computed protomer populations. The resulting protomer equilibrium is valuable, for example, in the context of electrospray ionization mass spectrometry where it may help identify the ionized species and assist the interpretation of the experiment. © 2017 Wiley Periodicals, Inc.

The gas phase fragmentation pathways of the nucleobase adenine upon 70 eV electron ionization are investigated by means of a combined stochastic and first-principles based molecular dynamics approach. We employ no preconceived fragmentation channels in our calculations, which simulate standard electron ionization mass spectrometry (EI-MS) conditions. The reactions observed compare well to a wealth of experimental and theoretical data available for this important nucleic acid building block. All significant peaks in the experimental mass spectrum of adenine are reproduced. Additionally, the fragment ion connectivities obtained from our simulations at least partially concur with results from previous experimental studies on selectively isotope labeled adenines. Moreover, we are able to assign noncyclic structures that are entropically favored and have not been proposed in nondynamic quantum chemical studies before to the decomposition products, which result automatically from our molecular dynamics procedure. From simulations under various conditions it is evident that most of the fragmentation reactions even at low internal excess energy (<10 eV) occur very fast within a few picoseconds.

Antineutrophil cytoplasmic antibodies (ANCA) are frequently associated with chronic inflammatory bowel diseases (IBD) and hepatobiliary disorders. However, their target antigens have not been identified yet. Recently, we observed an atypical perinuclear ANCA fluorescence (p-ANCA) together with an intranuclear staining using ANCA-positive sera from patients with IBD and hepatobiliary disorders. This observation suggests that the target antigens are localized within the nucleus of neutrophilic granulocytes. To further investigate this hypothesis, we examined sera from patients with ulcerative colitis, primary sclerosing cholangitis, autoimmune hepatitis or systemic vasculitis on ethanol or formaldehyde-fixed neutrophils using confocal laser scanning microscopy and immunoelectron microscopy. Counterstaining with propidium iodide, a DNA-specific dye, showed that ANCA-positive sera in IBD and heptobiliary disorders react with intranuclear antigens at the nuclear periphery of the neutrophils. Double immunolabeling techniques revealed that nuclear lamina proteins, lamins A, C and B1, and lamin B receptor were colocalized with the antigen(s) recognized by atypical p-ANCA. No colocalization was observed with classical p-ANCA and antibodies against histones (H1-H4). Our study showed that atypical p-ANCA are antinuclear antibodies reactive with granulocyte-specific antigens present in the nuclear lamina. (HEPATOLOGY 1998;28:332-340.)