cell2mol: encoding chemistry to interpret crystallographic data

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A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Factorized structure of the long-range two-electron integrals tensor and its application in quantum chemistry

Laura Grigori

We introduce two new approximation methods for the numerical evaluation of the long-range component of the range-separated Coulomb potential and the approximation of the resulting high dimensional Two-Electron Integrals tensor (TEI) with long-range interac ...

Academic Press Inc Elsevier Science2023

Modeling high-entropy transition metal alloys with alchemical compression

Michele Ceriotti, Sandip De, Nataliya Lopanitsyna, Guillaume André Jean Fraux

Alloys composed of several elements in roughly equimolar composition, often referred to as high-entropy alloys, have long been of interest for their thermodynamics and peculiar mechanical properties, and more recently for their potential application in cat ...

AMER PHYSICAL SOC2023

Salt Bridge Structure of Microhydrated Arginine Kinetically Trapped in the Gas Phase by Evaporative Cooling

Oleg Boyarkine, Andrei Zviagin

Aminoacids and peptides generally exhibit zwitterionic forms withsalt bridge (SB) structures in solution but charge-solvated (CS) motifsin the gas phase. Here, we report a study of non-covalent complexesof the protonated amino acid arginine, ArgH(+)(H2O)( ...

2023

De novo design of protein interactions with learned surface fingerprints

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Aaron Simone Petruzzella, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Alexandra Teslenko, Jane Marsden, Michael Bronstein, Casper Alexander Goverde, Stephen Michael Buckley, Dongchun Ni, Martin Pacesa

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

Plane Waves Versus Correlation-Consistent Basis Sets: A Comparison of MP2 Non-Covalent Interaction Energies in the Complete Basis Set Limit

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

Second-order Moller-Plesset perturbation theory (MP2) is the most expedient wave function-based method for considering electron correlation in quantum chemical calculations and, as such, provides a cost-effective framework to assess the effects of basis se ...

Amer Chemical Soc2023

New Cu (I) complexes as catalyst for "click" reaction: An experimental and computational study

Farzaneh Fadaei Tirani

In this work, two novel well-defined Cu (I) complexes of a Schiff base ligand are described. For this purpose, N, N '-bis (trans-cinnamaldehyde) ethylenediimine [C20H20N2] (L) and Cu (I) complex of the type [CuC20H20N2)PPh3Cl] (C1) and [Cu(C20H20N2)PPh3Br] ...

WILEY2023

Molecular simulation on two-dimensional nanoporous material for energy-efficient separation

Mohammad Tohidivahdat

The energy-consumption by the chemical and petrochemical industry in the European Union (EU) accounts for about quarter of its energy footprint. Approximately half of this energy goes toward chemical separation, currently dominated by thermally-driven pro ...

EPFL2023

Competition between Carrier Injection and Structural Distortions in Electron-Doped Perovskite Nickelate Thin Films

Jean-Marc Triscone, Duncan Thomas Lindsay Alexander, Jonathan Spring, Bernat Mundet

The discovery of superconductivity in doped infinite-layer nickelate thin films has brought increased attention to the behavior of the doped perovskite phase. Despite this interest, the majority of existing studies pertain to hole-doped perovskite rare-ear ...

WILEY2023

A Simple, Transition Metal Catalyst-Free Method for the Design of Complex Organic Building Blocks Used to Construct Porous Metal-Organic Frameworks

Jocelyn Richard Roth, Wendy Lee Queen, Ilia Kochetygov, Anita Justin, Till Marian Schertenleib, Jordi Espin Marti, Sophia Alessandra Pache, Nazanin Taheri

The design of metal-organic frameworks (MOFs) having large pore sizes and volumes often requires the use of complex organic ligands, currently synthesized using costly and time-consuming palladium-catalyzed coupling chemistry. Thus, in the present work, a ...

Wiley-VCH Verlag GmbH2023

Structural topology exploration through policy-based generation of equilibrium representations

Corentin Jean Dominique Fivet, Ioannis Mirtsopoulos

Mainstream approaches to design spatial architectural forms that are structurally relevant consist either in adapting well-known and catalogued conventional types or in searching for close-to-optimum solutions of well-defined problems. Few means exist to e ...

2023

Influence of aerosol acidity and organic ligands on transition metal solubility and oxidative potential of fine particulate matter in urban environments

Gerhard Lammel, Athanasios Nenes

The adverse health effects of air pollution around the world have been associated with the inhalation of fine particulate matter (PM2.5). Such outcomes are thought to be related to the induction of oxidative stress due to the excess formation of reactive o ...

Elsevier2023

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