Kohn-Sham inversion for open-shell systems.

Methods based on density-functional theory usually treat open-shell atoms and molecules within the spin-unrestricted Kohn-Sham (KS) formalism, which breaks symmetries in real and spin space. Symmetry breaking is possible because the KS Hamiltonian operator does not need to exhibit the full symmetry of the physical Hamiltonian operator, but only the symmetry of the spin density, which is generally lower. Symmetry breaking leads to spin contamination and prevents a proper classification of the KS wave function with respect to the symmetries of the physical electron system.

Mode of Metal Ligation Governs Inhibition of Carboxypeptidase A.

Carboxypeptidase is a Zn-dependent protease that specifically recognises and hydrolyses peptides with a hydrophobic side chain at the C-terminal residue. According to hydrolysis mechanisms proposed in the literature, catalysis requires a water molecule to be close to the Zn ion so as to be activated as a nucleophile. Among small molecules that resemble the slowly hydrolysed Gly-Tyr peptide, which have been previously designed as inhibitors and characterised structurally, a variant with the terminal amino acid in a D-configuration has been the most effective.

Coverage- and temperature-induced self-metalation of tetraphenyltransdibenzoporphyrin on Cu(111).

We have investigated the adsorption and self-metalation of free-base tetraphenyltransdibenzoporphyrin (2H-TPtdBP) on Cu(111) as a function of coverage and temperature using scanning tunneling microscopy, x-ray photoelectron spectroscopy, temperature programmed desorption, and density-functional theory calculations. At low coverages (<0.16 molecules nm), we observe isolated individual molecules with an inverted conformation and no self-metalation up to 363 K.

Model Catalytic Studies on the Thermal Dehydrogenation of the Benzaldehyde/Cyclohexylmethanol LOHC System on Pt(111).

We investigated the dehydrogenation reaction and the thermal robustness of the liquid organic hydrogen carrier (LOHC) couple benzaldehyde/cyclohexylmethanol on a Pt(111) model catalyst in situ in synchrotron radiation photoelectron spectroscopy- and complementary temperature-programmed desorption experiments. The system stores hydrogen in a cyclohexyl group and a primary alcohol functionality and achieves an attractive hydrogen storage capacity of 7.0 mass %.

An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package.

An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer-monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory-Huggins parameters and isotropic particle-particle repulsions for Dissipative Particle Dynamics (DPD).

Metal-insulator transition of spinless fermions coupled to dispersive optical bosons.

Including the previously ignored dispersion of phonons we revisit the metal-insulator transition problem in one-dimensional electron-phonon systems on the basis of a modified spinless fermion Holstein model. Using matrix-product-state techniques we determine the global ground-state phase diagram in the thermodynamic limit for the half-filled band case, and show that in particular the curvature of the bare phonon band has a significant effect, not only on the transport properties characterized by the conductance and the Luttinger liquid parameter, but also on the phase space structure of the model as a whole. While a downward curved (convex) dispersion of the phonons only shifts the Tomonaga-Luttinger-liquid to charge-density-wave quantum phase transition towards stronger EP coupling, an upward curved (concave) phonon band leads to a new phase-separated state which, in the case of strong dispersion, can even completely cover the charge-density wave.

Characterization of domain formation in complex membranes.

A widely known property of lipid membranes is their tendency to undergo a separation into disordered (L) and ordered (L) domains. This impacts the local structure of the membrane relevant for the physical (e.g.

Accurate NMR Shieldings with σ-Functionals.

In recent years, density-functional methods relying on a new type of fifth-rung correlation functionals called σ-functionals have been introduced. σ-Functionals are technically closely related to the random phase approximation and require the same computational effort but yield distinctively higher accuracies for reaction and transition state energies of main group chemistry and even outperform double-hybrid functionals for these energies. In this work, we systematically investigate how accurate σ-functionals can describe nuclear magnetic resonance (NMR) shieldings.

Unveiling the Multielectron Acceptor Properties of π-Expanded Pyracylene: Reversible Boat to Chair Conversion.

In this work, the chemical reduction of a hybrid pyracylene-hexa--hexabenzocoronene () nanographene was investigated with different alkali metals (Na, K, Rb) to reveal its remarkable multielectron acceptor abilities. The UV-vis and H NMR spectroscopy monitoring of the stepwise reduction reactions supports the existence of all intermediate reduction states up to the hexaanion for . Tuning the experimental conditions enabled the synthesis of the anions with gradually increasing reduction states (up to -5) isolated with different alkali metal ions as crystalline materials.

A concept of dual-responsive prodrugs based on oligomerization-controlled reactivity of ester groups: an improvement of cancer cells neutrophils selectivity of camptothecin.

Many known chemotherapeutic anticancer agents exhibit neutropenia as a dose-limiting side effect. In this paper we suggest a prodrug concept solving this problem for camptothecin (HO-cpt). The prodrug is programmed according to Boolean "AND" logic.

Basis Set Requirements of σ-Functionals for Gaussian- and Slater-Type Basis Functions and Comparison with Range-Separated Hybrid and Double Hybrid Functionals.

σ-Functionals belong to the class of Kohn-Sham (KS) correlation functionals based on the adiabatic-connection fluctuation-dissipation theorem and are technically closely related to the random phase approximation (RPA). They have the same computational demand as the latter, with the computational effort of an energy evaluation for both methods being lower than that of a preceding hybrid DFT calculation for typical systems but yield much higher accuracy, reaching chemical accuracy of 1 kcal/mol for quantities such as reactions and transition energies in main group chemistry. In previous work on σ-functionals, rather large Gaussian basis sets have been used.

In Silico Study of Camptothecin-Based Pro-Drugs Binding to Human Carboxylesterase 2.

Pro-drugs, which ideally release their active compound only at the site of action, i.e., in a cancer cell, are a promising approach towards an increased specificity and hence reduced side effects in chemotherapy.

Avoiding spin contamination and spatial symmetry breaking by exact-exchange-only optimized-effective-potential methods within the symmetrized Kohn-Sham framework.

For open-shell atoms and molecules, Kohn-Sham (KS) methods typically resort to spin-polarized approaches that exhibit spin-contamination and often break spatial symmetries. As a result, the KS Hamiltonian operator and the KS orbitals do not exhibit the space and spin symmetry of the physical electron system. The KS formalism can be symmetrized in a rigorous way only in real space, only in spin space, or both in real and spin space.

Bromination of 2D materials.

The adsorption, reaction and thermal stability of bromine on Rh(111)-supported hexagonal boron nitride (-BN) and graphene were investigated. Synchrotron radiation-based high-resolution x-ray photoelectron spectroscopy (XPS) and temperature-programmed XPS allowed us to follow the adsorption process and the thermal evolutionon the molecular scale. On-BN/Rh(111), bromine adsorbs exclusively in the pores of the nanomesh while we observe no such selectivity for graphene/Rh(111).

Speeding-up Hybrid Functional-Based Molecular Dynamics Using Multiple Time-stepping and Resonance-Free Thermostat.

molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at the level of generalized gradient approximation (GGA), which is at the second rung of DFT functionals in terms of accuracy. Hybrid DFT functionals, which form the fourth rung in the accuracy ladder, are not commonly used in AIMD simulations as the computational cost involved is 100 times or higher.

Computational Characterization of the Binding Properties of the HIV1-Neutralizing Antibody PG16 and Design of PG16-Derived CDRH3 Peptides.

PG16 is a broadly neutralizing antibody that binds to the gp120 subunit of the HIV-1 Env protein. The major interaction site is formed by the unusually long complementarity determining region (CDR) H3. The CDRH3 residue Tyr100H is known to represent a tyrosine sulfation site; however, this modification is not present in the experimental complex structure of PG16 with full-length HIV-1 Env.

Role of lipid nanodomains for inhibitory FcγRIIb function.

The inhibitory Fcγ receptor FcγRIIb is involved in immune regulation and is known to localize to specific regions of the plasma membrane called lipid rafts. Previous studies suggested a link between the altered lateral receptor localization within the plasma membrane and the functional impairment of the FcγRIIb-I232T variant that is associated with systemic lupus erythematosus. Here, we conducted microsecond all-atom molecular dynamics simulations and IgG binding assays to investigate the lipid nano-environment of FcγRIIb monomers and of the FcγRIIb-I232T mutant within a plasma membrane model, the orientation of the FcγRIIb ectodomain, and its accessibility to IgG ligands.

Computational Analysis of Histamine Protonation Effects on HR Binding.

Despite numerous studies investigating histamine and its receptors, the impact of histamine protonation states on binding to the histamine H1-receptor (H1R) has remained elusive. Therefore, we assessed the influence of different histamine tautomers (τ-tautomer, π-tautomer) and charge states (mono- vs. dicationic) on the interaction with the ternary histamine-H1R-G complex.

IDH3γ functions as a redox switch regulating mitochondrial energy metabolism and contractility in the heart.

Redox signaling and cardiac function are tightly linked. However, it is largely unknown which protein targets are affected by hydrogen peroxide (HO) in cardiomyocytes that underly impaired inotropic effects during oxidative stress. Here, we combine a chemogenetic mouse model (HyPer-DAO mice) and a redox-proteomics approach to identify redox sensitive proteins.

Immunoglobulin G-dependent inhibition of inflammatory bone remodeling requires pattern recognition receptor Dectin-1.

Immunoglobulin G (IgG) antibodies are major drivers of inflammation during infectious and autoimmune diseases. In pooled serum IgG (IVIg), however, antibodies have a potent immunomodulatory and anti-inflammatory activity, but how this is mediated is unclear. We studied IgG-dependent initiation of resolution of inflammation in cytokine- and autoantibody-driven models of rheumatoid arthritis and found IVIg sialylation inhibited joint inflammation, whereas inhibition of osteoclastogenesis was sialic acid independent.

Lipid Bicelles in the Study of Biomembrane Characteristics.

Simulations of lipid membranes typically make use of periodic boundary conditions to mimic macroscopically sized membranes and allow for comparison to experiments performed e.g. on planar lipid membranes or on unilamellar lipid vesicles.

Self-supervised machine learning pushes the sensitivity limit in label-free detection of single proteins below 10 kDa.

Interferometric scattering (iSCAT) microscopy is a label-free optical method capable of detecting single proteins, localizing their binding positions with nanometer precision, and measuring their mass. In the ideal case, iSCAT is limited by shot noise such that collection of more photons should extend its detection sensitivity to biomolecules of arbitrarily low mass. However, a number of technical noise sources combined with speckle-like background fluctuations have restricted the detection limit in iSCAT.

Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe /Fe Redox Reaction.

Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe /Fe ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE).

A previously unknown Argonaute 2 variant positively modulates the viability of melanoma cells.

In malignant melanoma, a highly aggressive form of skin cancer, many microRNAs are aberrantly expressed contributing to tumorigenesis and progression. Further, deregulation of microRNA processing enzymes, like the miRNA-binding protein Argonaute 2, significantly impacts microRNA function. This study characterizes a novel splice variant of Argonaut 2, AGO2-ex1/3.