RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data.

High-throughput characterization of antibody-antigen complexes at the atomic level is critical for understanding antibody function enabling therapeutic development. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) enables rapid epitope mapping, but its data are too sparse for independent structure determination. In this study, we introduce RosettaHDX, a hybrid method that combines computational docking with differential HDX-MS data to enhance the accuracy of antibody-antigen complex models beyond what either method can achieve individually.

Asymmetric Migratory Tsuji-Wacker Oxidation Enables the Enantioselective Synthesis of Hetero- and Isosteric Diarylmethanes.

Diarylmethanes play, in part, a pivotal role in the design of highly potent, chiral, nonracemic drugs whose bioactivity is typically affected by the substitution pattern of their arene units. In this context, certain arenes such as -substituted benzenes or unsubstituted heteroarenes cause particular synthetic challenges, since such isosteric residues at the central methane carbon atom are typically indistinguishable for a chiral catalyst. Hence, the stereoselective incorporation of isosteric (hetero)arenes into chiral methane scaffolds requires the use of stoichiometrically differentiated building blocks, which is typically realized through preceding redox-modifying operations such as metalation or halogenation and thus associated with disadvantageous step- and redox-economic traits.

Advanced Charge Extended Hückel (CEH) Model and a Consistent Adaptive Minimal Basis Set for the Elements = 1-103.

The Charge Extended Hückel (CEH) model, initially introduced for adaptive atomic orbital (AO) basis set construction ( , 159, 164108), has been significantly revised to enhance accuracy and robustness, particularly in challenging electronic situations. This revision includes an extension toward -elements, covering actinoids with their -electrons in the valence space. We present a novel noniterative approximation for the electrostatic contribution to the effective Fock matrix, which substantially improves performance in polar or charged systems.

Regioregular Poly(p-phenylene iminoborane): A Strictly Alternating BN-Isostere of Poly(p-phenylene vinylene) with Stimuli-Responsive Behavior.

Incorporation of BN units into π-conjugated organic compounds, as substitutes for specific CC couples, often leads to new hybrid materials with modified physical and chemical properties. Poly(p-phenylene iminoborane)s are derived from well-known poly(p-phenylene vinylene) (PPV) by replacement of the vinylene groups by B=N linking units. Herein, an unprecedented poly(p-phenylene iminoborane) is presented that features a strictly alternating sequence of BN units along the main chain.

A Discrete Trialane with a Near-Linear Al Axis.

The presence of inherent electronic unsaturation in aluminum predominantly results in the formation of aluminum clusters, with very few examples of compounds containing discrete chains of aluminum atoms in existence. In this work, we present the successful synthesis and structural authentication of a highly unusual trialane species with a near-linear chain of three Al atoms, alongside a carbene-stabilized aluminyl anion ([LAlR]), an alternative product produced by varying the reaction conditions. Quantum-chemical calculations have been applied to elucidate the electronic structure and bonding of these novel compounds.

Accelerated Mechanochemical Bond Scission and Stabilization against Heat and Light in Carbamoyloxime Mechanophores.

Current approaches to the discovery of mechanochemical reactions in polymers are limited by the interconnection of the zero-force and force-modified potential energy surfaces since most mechanochemical reactions are force-biased thermal reactions. Here, carbamoyloximes are developed as a mechanophore class in which the mechanochemical reaction rates counterintuitively increase together with the thermal stability. All carbamoyloxime mechanophores undergo force-induced homolytic bond scission at the N-O bond, and their mechanochemical scission rate increases with the degree of substitution on the α-substituent.

SpaiNN: equivariant message passing for excited-state nonadiabatic molecular dynamics.

Excited-state molecular dynamics simulations are crucial for understanding processes like photosynthesis, vision, and radiation damage. However, the computational complexity of quantum chemical calculations restricts their scope. Machine learning offers a solution by delivering high-accuracy properties at lower computational costs.

Unveiling Hierarchical Self-Assembly of Triazolylferrocenyl Dendrimers: Producing Non-Traditional Intrinsically Green Fluorescent Vesosomes for Nanotheranostics.

Dendrimers and supramolecular chemistry continue to fascinate researchers due to the endless unrevealed potential of their combination. This study investigates the self-assembly process of a series of hydrophobic triazolylferrocenyl dendrimers in aqueous medium. Deep investigation through NMR spectroscopy, absorption UV-vis spectroscopy along with theoretical simulations demonstrates that the ferrocenyl moieties interact intramolecularly and intermolecularly driving the self-assembly process.

Dark times: iminothioindoxyl--nucleoside fluorescence quenchers with defined location and minimal perturbation in DNA.

Fluorescence quenchers for application in DNA - like the BHQ family - tend to be large molecules which need to be attached, often post-synthetically, long linkers. In this study, we present two new iminothioindoxyl--nucleosidic quenchers which are very compact, feature a native backbone and can be introduced into DNA regular solid-phase synthesis. Especially with d as juxtaposed nucleobase, they have a defined location and orientation in a DNA duplex with minimal perturbation of the structure and hence interaction capabilities.

Deconvoluting XPS Spectra of La-Containing Perovskites from First-Principles.

Perovskite-based oxides are used in electrochemical CO and HO reduction in electrochemical cells due to their compositional versatility, redox properties, and stability. However, limited knowledge exists on the mechanisms driving these processes. Toward this understanding, herein we probe the core level binding energy shifts of water-derived adspecies (H, O, OH, HO) as well as the adsorption of CO on LaCoO and LaNiO and correlate the simulated peaks with experimental temperature-programmed X-ray photoelectron spectroscopy (TPXPS) results.

The Dual Mode of Antibacterial Action of the Synthetic Small Molecule DCAP Involves Lipid II Binding.

The synthetic small molecule DCAP is a chemically well-characterized compound with antibiotic activity against Gram-positive and Gram-negative bacteria, including drug-resistant pathogens. Until now, its mechanism of action was proposed to rely exclusively on targeting the bacterial membrane, thereby causing membrane depolarization, and increasing membrane permeability (Eun 2012, 134 (28), 11322-11325; Hurley 2015, 6, 466-471). Here, we show that the antibiotic activity of DCAP results from a dual mode of action that is more targeted and multifaceted than previously anticipated.

ΔDFT Predicts Inverted Singlet-Triplet Gaps with Chemical Accuracy at a Fraction of the Cost of Wave Function-Based Approaches.

Efficient OLEDs need to quickly convert singlet and triplet excitons into photons. Molecules with an inverted singlet-triplet energy gap (INVEST) are promising candidates for this task. However, typical INVEST molecules have drawbacks like too low oscillator strengths and excitation energies.

On the Interplay Between Force, Temperature, and Electric Fields in the Rupture Process of Mechanophores.

The use of oriented external electric fields (OEEFs) shows promise as an alternative approach to chemical catalysis. The ability to target a specific bond by aligning it with a bond-weakening electric field may be beneficial in mechanochemical reactions, which use mechanical force to selectively rupture bonds. Previous computational studies have focused on a static description of molecules in OEEFs, neglecting to test the influence of thermal oscillations on molecular stability.

A simple 230 MHz photodetector based on exfoliated WSe multilayers.

We demonstrate 230 MHz photodetection and a switching energy of merely 27 fJ using WSe multilayers and a very simple device architecture. This improvement over previous, slower WSe devices is enabled by systematically reducing the RC constant of devices through decreasing the photoresistance and capacitance. In contrast to MoS, reducing the WSe thickness toward a monolayer only weakly decreases the response time, highlighting that ultrafast photodetection is also possible with atomically thin WSe.

Observation of Interatomic Coulombic Decay Induced by Double Excitation of Helium in Nanodroplets.

Interatomic Coulombic decay (ICD) plays a crucial role in weakly bound complexes exposed to intense or high-energy radiation. So far, neutral or ionic atoms or molecules have been prepared in singly excited electron or hole states that can transfer energy to neighboring centers and cause ionization and radiation damage. Here we demonstrate that a doubly excited atom, despite its extremely short lifetime, can decay by ICD; evidenced by high-resolution photoelectron spectra of He nanodroplets excited to the 2s2p+ state.

A General Iron-Catalyzed Decarboxylative Oxygenation of Aliphatic Carboxylic Acids.

We report an iron-catalyzed decarboxylative C(sp)-O bond-forming reaction under mild, base-free conditions with visible light irradiation. The transformation uses readily available and structurally diverse carboxylic acids, iron photocatalyst, and 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO) derivatives as oxygenation reagents. The process exhibits a broad scope in acids possessing a wide range of stereoelectronic properties and functional groups.

OneFlowTraX: a user-friendly software for super-resolution analysis of single-molecule dynamics and nanoscale organization.

Super-resolution microscopy (SRM) approaches revolutionize cell biology by providing insights into the nanoscale organization and dynamics of macromolecular assemblies and single molecules in living cells. A major hurdle limiting SRM democratization is post-acquisition data analysis which is often complex and time-consuming. Here, we present OneFlowTraX, a user-friendly and open-source software dedicated to the analysis of single-molecule localization microscopy (SMLM) approaches such as single-particle tracking photoactivated localization microscopy (sptPALM).

Probing the Electronic Structure of [BH] Dianion Encapsulated by an Octamethylcalix[4]pyrrole Molecule.

Despite being an important -borate in condensed phase boron chemistry, isolated [BH] is electronically unstable and has never been detected in the gas phase. Herein, we report a successful capture of this fleeting species through binding with an octamethylcalix[4]pyrrole (omC4P) molecule to form a stable gaseous omC4P·[BH] complex and its characterizations utilizing negative ion photoelectron spectroscopy (NIPES). The recorded NIPE spectrum, contributed by both omC4P and [BH], is deconvoluted by subtracting the omC4P contribution to yield a [BH] spectrum.

JEDI: A versatile code for strain analysis of molecular and periodic systems under deformation.

Stretching or compression can induce significant energetic, geometric, and spectroscopic changes in materials. To fully exploit these effects in the design of mechano- or piezo-chromic materials, self-healing polymers, and other mechanoresponsive devices, a detailed knowledge about the distribution of mechanical strain in the material is essential. Within the past decade, Judgement of Energy DIstribution (JEDI) analysis has emerged as a useful tool for this purpose.

Electronic structure and transport in the potential Luttinger liquids CsNbBrS and RbNbBrS.

The crystal structures of ANbBrS (A = Rb and Cs) have been refined by single crystal X-ray diffraction, and are found to form highly anisotropic materials based on chains of the triangular Nb cluster core. The Nb cluster core contains seven valence electrons, six of them being assigned to Nb-Nb bonds within the Nb triangle and one unpaired d electron. The presence of this surplus electron gives rise to the formation of correlated electronic states.

Emergent Properties in Chemistry - Relating Molecular Properties to Bulk Behavior.

Certain properties of an object only emerge when a sufficient number of those objects are present in a definite arrangement. For example, one or two water molecules cannot said to be in a liquid state, but a drop of water can be. This concept of emergence has been studied extensively, but only occasionally discussed explicitly in the context of chemistry.

CREST-A program for the exploration of low-energy molecular chemical space.

Conformer-rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys.

Benchmark Study on the Calculation of Pb NMR Chemical Shifts.

A benchmark set for the computation of Pb nuclear magnetic resonance (NMR) chemical shifts is presented. The set includes conformer ensembles of 50 lead-containing molecular compounds and their experimentally measured Pb NMR chemical shifts. Various bonding motifs at the Pb center with up to seven bonding partners are included.