T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery.

Effective, unbiased, high-throughput methods to functionally identify both class II and class I HLA-presented T cell epitopes and their cognate T cell receptors (TCRs) are essential for and prerequisite to diagnostic and therapeutic applications, yet remain underdeveloped. Here, we present T-FINDER [T cell Functional Identification and (Neo)-antigen Discovery of Epitopes and Receptors], a system to rapidly deconvolute CD4 and CD8 TCRs and targets physiologically processed and presented by an individual's unmanipulated, complete human leukocyte antigen (HLA) haplotype. Combining a highly sensitive TCR signaling reporter with an antigen processing system to overcome previously undescribed limitations to target expression, T-FINDER both robustly identifies unknown peptide:HLA ligands from antigen libraries and rapidly screens and functionally validates the specificity of large TCR libraries against known or predicted targets.

CO on Graphene: Benchmarking Computational Approaches to Noncovalent Interactions.

Designing and optimizing graphene-based gas sensors entail constructing appropriate atomistic representations for the physisorption complex of an analyte on an infinite graphene sheet, then selecting accurate yet affordable methods for geometry optimizations and energy computations. In this work, diverse density functionals (DFs), coupled cluster theory, and symmetry-adapted perturbation theory (SAPT) in conjunction with a range of finite and periodic surface models of bare and supported graphene were tested for their ability to reproduce the experimental adsorption energies of CO on graphene in a low-coverage regime. Periodic results are accurately reproduced by the interaction energies extrapolated from finite clusters to infinity.

Metal-Free Molecular Catalysts for the Oxygen Reduction Reaction: Electron Affinity as an Activity Descriptor.

Heteroatom-doped polyaromatic hydrocarbons (or nanographenes) are promising molecular electrocatalysts for the oxygen reduction reaction (ORR). Here, we use density functional theory to investigate the first step of the ORR pathway (chemisorption) for a set of molecules with experimentally determined catalytic activities. Weak chemisorption is found for only negatively charged catalysts, and a strong correlation is observed between the computed electron affinities and experimental catalytic activities for a range of B- and B,N-doped polyaromatic hydrocarbons.

Why Ultrafast Photoinduced CO Desorption Dominates over Oxidation on Ru(0001).

CO oxidation on Ru(0001) is a long-standing example of a reaction that, being thermally forbidden in ultrahigh vacuum, can be activated by femtosecond laser pulses. In spite of its relevance, the precise dynamics of the photoinduced oxidation process as well as the reasons behind the dominant role of the competing CO photodesorption remain unclear. Here we use ab initio molecular dynamics with electronic friction that account for the highly excited and nonequilibrated system created by the laser to investigate both reactions.

Stereoinversion of tetrahedral p-block element hydrides.

The potential energy surfaces of 15 tetrahedral p-block element hydrides were screened on the multireference level. It was addressed whether stereoinversion competes against other reactions, such as reductive H-elimination or hydride loss, and if so, along which pathway the stereomutation occurs. Importantly, stereoinversion transition structures for the ammonium cation (C) and the tetrahydridoborate anion (C) were identified for the first time.

Dioxygen Activation and Pyrrole α-Cleavage with Calix[4]pyrrolato Aluminates: Enzyme Model by Structural Constraint.

The present work describes the reaction of triplet dioxygen with the porphyrinogenic calix[4]pyrrolato aluminates to alkylperoxido aluminates in high selectivity. Multiconfigurational quantum chemical computations disclose the mechanism for this spin-forbidden process. Despite a negligible spin-orbit coupling constant, the intersystem crossing (ISC) is facilitated by singlet and triplet state degeneracy and spin-vibronic coupling.

PSIXAS: A Psi4 plugin for efficient simulations of X-ray absorption spectra based on the transition-potential and Δ-Kohn-Sham method.

Near edge X-ray absorption fine structure (NEXAFS) spectra and their pump-probe extension (PP-NEXAFS) offer insights into valence- and core-excited states. We present PSIXAS, a recent implementation for simulating NEXAFS and PP-NEXAFS spectra by means of the transition-potential and the Δ-Kohn-Sham method. The approach is implemented in form of a software plugin for the Psi4 code, which provides access to a wide selection of basis sets as well as density functionals.

Iron doped gold cluster nanomagnets: determination of barriers for demagnetization.

Magnetic properties of small- and nano-sized iron doped gold clusters are calculated at the level of second order multireference perturbation theory. We first assess the methodology for small AuFe and AuFe clusters, which are representative of even and odd electron count systems. We find that larger active spaces are needed for the odd electron count system, AuFe, which exhibits isotropic magnetization behaviour.

An efficient first principles method for molecular pump-probe NEXAFS spectra: Application to thymine and azobenzene.

Pump-probe near edge X-ray absorption fine structure (PP-NEXAFS) spectra of molecules offer insight into valence-excited states, even if optically dark. In PP-NEXAFS spectroscopy, the molecule is "pumped" by UV or visible light enforcing a valence excitation, followed by an X-ray "probe" exciting core electrons into (now) partially empty valence orbitals. Calculations of PP-NEXAFS have so far been done by costly, correlated wavefunction methods which are not easily applicable to medium-sized or large molecules.

Control of Oxidation and Spin State in a Single-Molecule Junction.

The oxidation and spin state of a metal-organic molecule determine its chemical reactivity and magnetic properties. Here, we demonstrate the reversible control of the oxidation and spin state in a single Fe porphyrin molecule in the force field of the tip of a scanning tunneling microscope. Within the regimes of half-integer and integer spin state, we can further track the evolution of the magnetocrystalline anisotropy.

The quest for best suited references for configuration interaction singles calculations of core excited states.

Near edge X-ray absorption fine structure (NEXAFS) simulations based on the conventional configuration interaction singles (CIS) lead to excitation energies, which are systematically blue shifted. Using a (restricted) open shell core hole reference instead of the Hartree Fock (HF) ground state orbitals improves (Decleva et al., Chem.

Systematic Investigation into the Matsuda-Heck Reaction of α-Methylene Lactones: How Conformational Constraints Direct the β-H-Elimination Step.

α-Methylene-γ-butyrolactone and α-methylene-δ-valerolactone undergo Pd-catalyzed Matsuda-Heck couplings with arene diazonium salts to α-benzyl butenolides or pentenolides, respectively, or to α-benzylidene lactones. The observed regioselectivity is strongly ring size dependent, with six-membered rings giving exclusively α-benzyl pentenolides, whereas the five-membered α-methylene lactone reacts to mixtures of regioisomers with a high proportion of (E)-α-benzylidene-γ-butyrolactones. DFT calculations suggest that the reasons for these differences are not thermodynamic but kinetic in nature.

A detailed assignment of NEXAFS resonances of imidazolium based ionic liquids.

In Near Edge X-Ray Absorption Fine Structure (NEXAFS) spectroscopy X-Ray photons are used to excite tightly bound core electrons to low-lying unoccupied orbitals of the system. This technique offers insight into the electronic structure of the system as well as useful structural information. In this work, we apply NEXAFS to two kinds of imidazolium based ionic liquids ([C(n)C1im](+)[NTf2](-) and [C4C1im](+)[I](-)).

C K-edge NEXAFS spectra of graphene with physical and chemical defects: a study based on density functional theory.

Recently, C K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of graphite (HOPG) surfaces have been measured for the pristine material, and for HOPG treated with either bromine or krypton plasmas (Lippitz et al., Surf. Sci.