Locuaz: an in silico platform for protein binders optimization.

Motivation: Engineering high-affinity binders targeting specific antigenic determinants remains a challenging and often daunting task, requiring extensive experimental screening. Computational methods have the potential to accelerate this process, reducing costs and time, but only if they demonstrate broad applicability and efficiency in exploring mutations, evaluating affinity, and pruning unproductive mutation paths.

Results: In response to these challenges, we introduce a new computational platform for optimizing protein binders towards their targets.

Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔ Predictions.

The development of highly potent antibodies and antibody fragments as binding agents holds significant implications in fields such as biosensing and biotherapeutics. Their binding strength is intricately linked to the arrangement and composition of residues at the binding interface. Computational techniques offer a robust means to predict the three-dimensional structure of these complexes and to assess the affinity changes resulting from mutations.

Use of Gaussian-Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory.

The electronic stopping power is an observable property that quantifies the ability of swift ions to penetrate matter to transfer energy to the electron cloud. The recent literature has proven the value of Real-Time Time-Dependent Density Functional Theory to accurately evaluate this property from first-principles, but questions remain regarding the capability of computer codes relying on atom-centered basis functions to capture the physics at play. In this Perspective, we draw attention to the fact that irradiation by swift ions triggers electron emission into the continuum, especially at the Bragg peak.

In-depth theoretical understanding of the chemical interaction of aromatic compounds with a gold nanoparticle.

Gold Nanoparticles (GNPs), owing to their unique properties and versatile preparation strategy, have been demonstrated to exhibit promising applications in diverse fields, which include bio-sensors, catalysts, nanomedicines and radiotherapy. Yet, the nature of the interfacial interaction of GNPs with their chemical environment remains elusive. Experimental vibrational spectroscopy can reveal different interactions of aromatic biological molecules absorbed on GNPs, that may result from changes in the orientation of the molecule.

Probing the structural properties of the water solvation shell around gold nanoparticles: A computational study.

While subjected to radiation, gold nanoparticles (GNPs) have been shown to enhance the production of radicals when added to aqueous solutions. It has been proposed that the arrangement of water solvation layers near the water-gold interface plays a significant role. As such, the structural and electronic properties of the first water solvation layer surrounding GNPs of varying sizes were compared to bulk water using classical molecular dynamics and quantum and semi-empirical methods.

Highly Crystalline K-Intercalated Polymeric Carbon Nitride for Visible-Light Photocatalytic Alkenes and Alkynes Deuterations.

In addition to the significance of photocatalytic hydrogen evolution, the utilization of the in situ generated H/D (deuterium) active species from water splitting for artificial photosynthesis of high value-added chemicals is very attractive and promising. Herein, photocatalytic water splitting technology is utilized to generate D-active species (i.e.

Graphene-Oxide-Catalyzed Direct CH-CH-Type Cross-Coupling: The Intrinsic Catalytic Activities of Zigzag Edges.

The development of graphene oxide (GO)-based materials for C-C cross-coupling represents a significant advance in carbocatalysis. Although GO has been used widely in various catalytic reactions, the scope of reactions reported is quite narrow, and the relationships between the type of functional groups present and the specific activity of the GO are not well understood. Herein, we explore CH-CH-type cross-coupling of xanthenes with arenes using GO as real carbocatalysts, and not as stoichiometric reactants.

A Step-by-Step Assembly of a 3D Coordination Polymer in the Solid-State by Desolvation and [2+2] Cycloaddition Reactions.

Two solid-state structural transformations that occur in a stepwise and a controlled manner are described. A combination of desolvation and cycloaddition reactions has been employed to synthesise a 3D coordination polymer (CP) from 1D CP [Cd(bdc)(4-spy)2 (H2 O)]⋅2 H2 O⋅2 DMF (bdc=1,4-benzenedicarboxylate, 4-spy=4-styrylpyridine) presumably via a 2D layered structure, [Cd2 (bdc)2 (4-spy)4 ]. In the absence of single crystals to follow the course of the photocycloaddition reaction, thermogravimetry, XAFS and NOESY NMR experiments were used to propose the formation of layered and pillared layered structures.

Tandem catalysis of amines using porous graphene oxide.

Porous graphene oxide can be used as a metal-free catalyst in the presence of air for oxidative coupling of primary amines. Herein, we explore a GO-catalyzed carbon-carbon or/and carbon-heteroatom bond formation strategy to functionalize primary amines in tandem to produce a series of valuable products, i.e.

Assembly of 3D coordination polymers from 2D sheets by [2+2] cycloaddition reaction.

The synthesis of three 2D interdigitated Zn(II) coordination polymers (CPs), by using three monotopic ligands containing C=C bonds, is reported. Among these, two CPs with 4spy (4-styryl pyridine) and 2F-4spy (a 2'-fluoro derivative of 4spy) ligands showed quantitative formation of cyclobutane rings, thus demonstrating a unique synthetic procedure to synthesize metal-organic frameworks (MOFs) by using this photochemical reaction. Interestingly, these compounds can also be synthesized by mechanochemical grinding procedures by using Zn(OAc)2.