Computational chemistry articles within Nature Communications

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  • Article
    | Open Access

    Tripartite-motif containing (TRIM) proteins modulate cellular responses to viral infection. Here the authors use molecular dynamics simulations to demonstrate that TRIM5α uses a two-dimensional lattice hopping mechanism to aggregate on the HIV capsid surface and initiate lattice growth.

    • Alvin Yu
    • , Katarzyna A. Skorupka
    •  & Gregory A. Voth

  • Article
    | Open Access

    Elctrochemical water splitting is of vital significance for energy conversion and storage. Here the authors show an electrocatalyst based on amorphous ruthenium-tellurium porous nanorods which exhibit significantly improved OER performance than its crystalline counterparts

    • Juan Wang
    • , Lili Han
    •  & Xiaoqing Huang

  • Article
    | Open Access

    While main group elements possess four valence orbitals that are accessible for bonding, quadruple bonding to main group elements is very rarely observed. Here the authors report that boron is able to form four bonding interactions with iron in the BFe(CO)3- anion complex.

    • Chaoxian Chi
    • , Jia-Qi Wang
    •  & Jun Li

  • Article
    | Open Access

    Practical calculations of molecular inelastic collisions are computationally very demanding. Here the authors use full-dimensional quantum scattering to calculate energy transfer probabilities in inelastic collision between hydrogen fluoride molecules successfully checked by available experimental vibrational quenching rate.Practical calculations of molecular inelastic collisions are computationally very demanding. Here the authors use full-dimensional quantum scattering to calculate energy transfer probabilities in inelastic collision between hydrogen fluoride molecules successfully checked by available experimental vibrational quenching rate.

    • Dongzheng Yang
    • , Jing Huang
    •  & Daiqian Xie

  • Article
    | Open Access

    Single-atom catalysts are widely investigated heterogeneous catalysts; however, the identification of the local environment of single atoms under experimental conditions is still challenging. Here, the authors clearly demonstrate that Rh single atoms adapt their local coordination and reactivity in response to various redox conditions.

    • Yan Tang
    • , Chithra Asokan
    •  & Philippe Sautet

  • Article
    | Open Access

    Prediction of stable clusters based on the jellium model is limited because of the usual assumption of their spherical symmetry. Here the authors propose a symmetry adapted orbital model by quantum chemistry calculations for the prediction of stable clusters with various shapes that obey a certain periodicity.

    • Takamasa Tsukamoto
    • , Naoki Haruta
    •  & Kimihisa Yamamoto

  • Article
    | Open Access

    Composite metal-organic framework materials can display useful synergetic properties, but typically suffer from disordered interfaces. Here the authors computationally identify optimal MOF pairings, looking at specific interactions between linkers and nodes, and synthesize six single crystal MOF@MOF composites.

    • Ohmin Kwon
    • , Jin Yeong Kim
    •  & Jihan Kim

  • Article
    | Open Access

    Nitro(hetero) arenes are valuable intermediates in organic synthesis, therefore mild and safe methods to nitrate C-H bonds remain desirable. Here, the authors report a bench-stable, inexpensive, easy to synthesize and recyclable nitrating reagent based on saccharin, allowing for nitration of (hetero)arenes with broad scope.

    • Roxan Calvo
    • , Kun Zhang
    •  & Dmitry Katayev

  • Article
    | Open Access

    Based on computations, the authors show that voltage stability of battery electrolytes is determined not by a single component but by formation of charge transfer complexes between salt anions and solvent molecules. A physical model is proposed and validated on several common electrolyte compositions.

    • Eric R. Fadel
    • , Francesco Faglioni
    •  & Boris Kozinsky

  • Article
    | Open Access

    The structural origin of the mid-gap states responsible for the time-dependent resistance drift in phase-change materials is still under debate. Here the authors use machine learning and density functional theory to identify the structural motifs of the mid-gap defects in the prototypical Ge2Sb2Te5 phase-change alloy.

    • Konstantinos Konstantinou
    • , Felix C. Mocanu
    •  & Stephen R. Elliott

  • Article
    | Open Access

    Computational modelling of chemical systems requires a balance between accuracy and computational cost. Here the authors use transfer learning to develop a general purpose neural network potential that approaches quantum-chemical accuracy for reaction thermochemistry, isomerization, and drug-like molecular torsions.

    • Justin S. Smith
    • , Benjamin T. Nebgen
    •  & Adrian E. Roitberg

  • Article
    | Open Access

    Enzyme substrates and products often diffuse too rapidly to assess the catalytic implications of these movements. Here, the authors characterise the structural basis of product and substrate diffusion for an exo-hydrolase and discover a substrate-product assisted processive catalytic mechanism.

    • Victor A. Streltsov
    • , Sukanya Luang
    •  & Maria Hrmova

  • Article
    | Open Access

    The origins of the different charging processes observed in graphene and boron-nitride nanofluidics are still under debate. Here, using ab-initio molecular dynamics, the authors show that hydroxide species in water exhibits physisorption on graphene but strong chemisorption on boron-nitride.

    • Benoît Grosjean
    • , Marie-Laure Bocquet
    •  & Rodolphe Vuilleumier

  • Article
    | Open Access

    Considering the large number of existing synthesised and hypothesised metal-organic frameworks, determining which materials perform best for given applications remains a challenge. Here, the authors screen the usable hydrogen uptake capacities of nearly 500,000 MOFs, and find that three frameworks outperform the current record-holder.

    • Alauddin Ahmed
    • , Saona Seth
    •  & Donald J. Siegel

  • Article
    | Open Access

    Thermally activated delayed fluorescence is a mechanism for enhancing the efficiency of organic light emitting diodes by harvesting triplet excitons, but there is still a need to design more efficient materials. Here, the authors rationally design and characterize a series of π-extended boron- and nitrogen-doped nanographenes as promising candidates.

    • Anton Pershin
    • , David Hall
    •  & Yoann Olivier

  • Article
    | Open Access

    While the conversion of greenhouse CO2 to chemical fuels offers a promising renewable energy technology, there is a dire need for new materials. Here, authors report the largest CO2 photocathode search using a first-principles approach to identify both known and unreported candidate photocatalysts.

    • Arunima K. Singh
    • , Joseph H. Montoya
    •  & Kristin A. Persson

  • Article
    | Open Access

    Halogen bonding can be exploited for the design of functional supramolecular materials, but heavier elements that are known to accept a halogen bond remain limited. Here, the authors demonstrate the formation of two-component cocrystals based on halogen bonds with phosphorus, arsenic and antimony.

    • Katarina Lisac
    • , Filip Topić
    •  & Dominik Cinčić

  • Article
    | Open Access

    CO2 conversion to reduced products provides a use for greenhouse gases, but reaction complexity stymies mechanistic studies. Here, authors present a microkinetic model for CO2 and CO reduction on copper, based on ab initio simulations, to elucidate pH’s impact on competitive reaction pathways.

    • Xinyan Liu
    • , Philomena Schlexer
    •  & Karen Chan

  • Article
    | Open Access

    Phase-change materials are applied as thermoelectric converters and battery electrodes, but underlying mechanisms are not fully understood. Here, the authors comprehensively describe thermal transport mechanisms of lithium sulfide based on molecular dynamics and first-principles simulations.

    • Yanguang Zhou
    • , Shiyun Xiong
    •  & Ming Hu

  • Article
    | Open Access

    Myoglobin bound to carbon monoxide undergoes an ultrafast light-induced reaction, which ends up in a photolyzed carbon monoxide and a spin transition of the iron center. Here, the authors employ quantum wavepacket dynamics to show that photolysis precedes the spin transition, a mechanism dominated by strong electron-nuclear couplings.

    • Konstantin Falahati
    • , Hiroyuki Tamura
    •  & Miquel Huix-Rotllant

  • Article
    | Open Access

    No substances with greater degrees of degeneracy than spherical atoms are known, due to geometrical limitations. In this work the authors combine density functional theory and tight-binding models to predict metal clusters with higher-fold degeneracies than spherical atoms, which are ascribed to dynamical symmetry.

    • Naoki Haruta
    • , Takamasa Tsukamoto
    •  & Kimihisa Yamamoto

  • Article
    | Open Access

    Supramolecular assemblies remain of great importance to a variety of fields, yet their targeted design and synthesis remains highly challenging. Here, Cooper and colleagues combine computational screening with high-throughput robotic synthesis and discover 33 new organic cage molecules that form cleanly in one-pot syntheses.

    • R. L. Greenaway
    • , V. Santolini
    •  & A. I. Cooper

  • Article
    | Open Access

    Detailed knowledge of how strain influences catalytic reactions remains elusive. Here, the authors experimentally measure the strain in supported Pt nanoparticles on alumina and ceria with atomic resolution and computationally explore how the strain affects the CO oxidation reaction.

    • Torben Nilsson Pingel
    • , Mikkel Jørgensen
    •  & Eva Olsson

  • Article
    | Open Access

    Minor variations in synthesis conditions can redirect crystallization pathways through different nonequilibrium intermediates. Here, the authors present a theoretical framework to predict which polymorphs appear during MnO2 precipitation, which is validated by in situ X-ray scattering of reaction progression.

    • Bor-Rong Chen
    • , Wenhao Sun
    •  & Laura T. Schelhas

  • Article
    | Open Access

    Deciphering absolute configuration of individual molecules directly by visual inspection remains a highly attractive goal. Here, the authors determine the absolute configuration and orientation of a single [123]tetramantane molecule adsorbed on Cu(111) using low temperature atomic force microscopy with a CO-functionalized tip.

    • Daniel Ebeling
    • , Marina Šekutor
    •  & Peter R. Schreiner

  • Article
    | Open Access

    Trial-and-error methods to identify suitable ligands for transition metal catalysis are time-consuming and costly. Here, the authors developed a combined experimental and computational approach to design chiral ligands for the enantioselective Markovnikov hydroboration of aliphatic terminal alkenes.

    • Hiroaki Iwamoto
    • , Tsuneo Imamoto
    •  & Hajime Ito

  • Article
    | Open Access

    Paramagnetic metal clusters with large ground spin states often possess attractive magnetic behaviors for information storage or solid-state cooling applications. Here, the authors design a giant {Ni21Gd20} cage, which using quantum monte carlo simulations they predict to possess a spin ground state approaching S = 91.

    • Wei-Peng Chen
    • , Jared Singleton
    •  & Yan-Zhen Zheng

  • Article
    | Open Access

    Understanding host–guest interactions and structural changes within porous materials is crucial for enhancing gas storage properties. Here, the authors combine cryogenic loading of gases with high pressure crystallography and computational techniques to obtain atomistic detail of adsorption-induced structural and energetic changes in ZIF-8.

    • Claire L. Hobday
    • , Christopher H. Woodall
    •  & Stephen A. Moggach

  • Article
    | Open Access

    While transition metal complexes bearing terminal oxido ligands are common, those of group 11 elements have yet to be experimentally observed. Here, Riedel and colleagues synthesise molecular oxygen fluorides of copper, silver and gold, and show that the oxo ligands possess radical character.

    • Lin Li
    • , Tony Stüker
    •  & Sebastian Riedel

  • Article
    | Open Access

    Molecular dynamics models for predicting the behavior of metallic nanostructures typically do not take into account polarization effects in metals. Here, the authors introduce a polarizable Lennard–Jones potential that provides quantitative insight into the role of induced charges at metal surfaces and related complex material interfaces.

    • Isidro Lorenzo Geada
    • , Hadi Ramezani-Dakhel
    •  & Hendrik Heinz

  • Article
    | Open Access

    The electron affinity of liquid water is a fundamental property which has not yet been accurately measured. Here, the authors predict this property by coupling path-integral molecular dynamics with ab initio potentials and electronic structure calculations, revisiting several estimates used in the literature.

    • Alex P. Gaiduk
    • , Tuan Anh Pham
    •  & Giulia Galli

  • Article
    | Open Access

    Clay is thought to have played a part in the origin of life. Here, the authors show that layered double hydroxides, a type of clay little studied despite its presumed prevalence on the early Earth, can facilitate the formation of small proteins.

    • Valentina Erastova
    • , Matteo T. Degiacomi
    •  & H. Chris Greenwell

  • Article
    | Open Access

    Stabilization of gold nanoclusters in order to prevent their self-aggregation remains a great challenge. Here, the authors describe transient stabilization of very small catalytic gold subnanoclusters by alkyl chains or aromatic groups appended to the reactive π bond of simple alkynes.

    • Jesús Cordón
    • , Gonzalo Jiménez-Osés
    •  & Miguel Monge

  • Article
    | Open Access

    Machine learning allows electronic structure calculations to access larger system sizes and, in dynamical simulations, longer time scales. Here, the authors perform such a simulation using a machine-learned density functional that avoids direct solution of the Kohn-Sham equations.

    • Felix Brockherde
    • , Leslie Vogt
    •  & Klaus-Robert Müller

  • Article
    | Open Access

    Identifying pathways and transition states is critical to understanding chemical and biological reactions. Here, the authors introduce a capable computational approach using conformational space annealing to find multiple reaction pathways via global optimization of the Onsager-Machlup action.

    • Juyong Lee
    • , In-Ho Lee
    •  & Bernard R. Brooks

  • Article
    | Open Access

    Machine learning is an increasingly popular approach to analyse data and make predictions. Here the authors develop a ‘deep learning’ framework for quantitative predictions and qualitative understanding of quantum-mechanical observables of chemical systems, beyond properties trivially contained in the training data.

    • Kristof T. Schütt
    • , Farhad Arbabzadah
    •  & Alexandre Tkatchenko

  • Article
    | Open Access

    Nematic liquid crystals have potential as sensors for various molecules. Here, the authors present a computational chemistry model for describing the detection of a warfare agent by liquid crystals, opening the door for the atomic-scale design of sensitive and selective chemoresponsive systems.

    • Luke T. Roling
    • , Jessica Scaranto
    •  & Manos Mavrikakis

  • Article
    | Open Access

    The pH dependence of the activity of Escherichia colimain sodium-proton antiporter NhaA is still not fully understood. Here, the authors use continuous constant pH molecular dynamics simulations to identify NhaA proton carrier residues and elucidate its gating and ion transport processes.

    • Yandong Huang
    • , Wei Chen
    •  & Jana Shen

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