Theoretical chemistry articles within Nature Communications

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  • 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

    Ionic liquid electrolytes can impart increased operational voltage and energy density in supercapacitors, but water may diminish performance. Here the authors show that the hydrophilicity/hydrophobicity of ionic liquids can influence electrosorption of water and ultimately the supercapacitor performance.

    • Sheng Bi
    • , Runxi Wang
    •  & Guang Feng

  • Article
    | Open Access

    Tautomerization of imines into enamines is the basis of their similar reactivity; however, minor structural changes may lead to different outcomes. Here, the authors show that the reaction of cyclohexanone and amines in presence of TEMPO affords either α-amino-enones or arylamines depending on the intermediate imine structure.

    • Xiaoming Jie
    • , Yaping Shang
    •  & Weiping Su

  • Article
    | Open Access

    While chemical bonding between carbon and the d- and p-block elements is relatively well-studied, that between carbon and the f-block elements remains comparatively poorly understood. Here, the authors synthesize a series of uranium−carbone complexes in which carbon forms an unprecedented double dative bond to uranium.

    • Wei Su
    • , Sudip Pan
    •  & Congqing Zhu

  • 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

    Manipulation of the photochemistry of molecules is traditionally achieved through synthetic chemical modifications. Here the authors use computational photochemistry to show how to control azobenzene photoisomerization through hybrid light–molecule states (polaritons).

    • J. Fregoni
    • , G. Granucci
    •  & S. Corni

  • Article
    | Open Access

    Solid-state nuclear magnetic resonance combined with quantum chemical shift predictions is limited by high computational cost. Here, the authors use machine learning based on local atomic environments to predict experimental chemical shifts in molecular solids with accuracy similar to density functional theory.

    • Federico M. Paruzzo
    • , Albert Hofstetter
    •  & Lyndon Emsley

  • 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

    With the rapid development of quantum computers, quantum machine learning approaches are emerging as powerful tools to perform electronic structure calculations. Here, the authors develop a quantum machine learning algorithm, which demonstrates significant improvements in solving quantum many-body problems.

    • Rongxin Xia
    •  & Sabre Kais

  • Article
    | Open Access

    Understanding fundamental processes that occur using solar-to-fuel conversion materials is crucial for constructing effective renewable energy collection. Here, authors find the hydrogen peroxide light-driven hole-scavenging mechanism over haematite to proceed with two active sites rather than one

    • Yotam Y. Avital
    • , Hen Dotan
    •  & Arik Yochelis

  • Article
    | Open Access

    Simultaneous accurate and efficient prediction of molecular properties relies on combined quantum mechanics and machine learning approaches. Here the authors develop a flexible machine-learning force-field with high-level accuracy for molecular dynamics simulations.

    • Stefan Chmiela
    • , Huziel E. Sauceda
    •  & Alexandre Tkatchenko

  • Article
    | Open Access

    Crystal stability prediction is of paramount importance for novel material discovery, with theoretical approaches alternative to expensive standard schemes highly desired. Here the authors develop a deep learning approach which, just using two descriptors, provides crystalline formation energies with very high accuracy.

    • Weike Ye
    • , Chi Chen
    •  & Shyue Ping Ong

  • 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

    Water uptake of natural polymers is accompanied by swelling and changes in the internal structure of the polymeric system but the exact mechanism of water-uptake and swelling remained unknown. Here the authors use atom-scale simulations to identify a molecular mechanism which is responsible for hysteresis in sorption-induced swelling in natural polymers.

    • Mingyang Chen
    • , Benoit Coasne
    •  & Jan Carmeliet

  • Article
    | Open Access

    Controllable synthesis of single atom catalysts with sufficiently high metal loading remains challenging due to the tendency of agglomeration. Here the authors synthesize a series of stable atomically dispersed cobalt atoms on graphene with high Co loadings via the regeneration of active sites by atomic layer deposition.

    • Huan Yan
    • , Xiaoxu Zhao
    •  & Jiong Lu

  • Article
    | Open Access

    Metal-support interaction plays an important role in heterogeneous catalysis, but silica has been rarely reported as an effective support to create active metal-support interfaces for promoting catalytic reactions. Here, the authors discover that Cu/SiO2 interface creates an exceptional effect to promote catalytic hydrogenation of esters.

    • Chaofa Xu
    • , Guangxu Chen
    •  & Nanfeng Zheng

  • Article
    | Open Access

    Radialenes have distinct structural, electronic and chemical properties from other hydrocarbons, but their synthesis remains a challenge. Here, the authors report a copper catalyzed one-step synthetic protocol of [4]radialene via the cyclotetramerization of phenylacetylene molecules upon thermal activation.

    • Qing Li
    • , Jianzhi Gao
    •  & Minghu Pan

  • Article
    | Open Access

    The description of van der Waals interactions should often account for coupling with pervasive electric fields, but this effect has been omitted in atomistic simulations. Here, the authors develop a model to study the effects of external charge on long-range van der Waals interactions.

    • Andrii Kleshchonok
    •  & Alexandre Tkatchenko

  • 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

    Developing robust catalysts for alkyne semi-hydrogenation remains a challenge. Here, the authors introduce a scalable protocol to prepare crystal phase and orientation controlled Pd3S nanoparticles supported on carbon nitride, exhibiting unparalleled semi-hydrogenation performance due to a high density of active and selective ensembles.

    • Davide Albani
    • , Masoud Shahrokhi
    •  & Javier Pérez-Ramírez

  • 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

    Heteroatom doping of buckybowls is a viable route to tune their intrinsic physico-chemical properties, but their synthesis remains challenging. Here, the authors report on a combined in-solution and on-surface synthetic strategy towards the fabrication of a buckybowl containing two fused nitrogen-doped pentagonal rings.

    • Shantanu Mishra
    • , Maciej Krzeszewski
    •  & Daniel T. Gryko

  • Article
    | Open Access

    The current industrial ammonia synthesis relies on the Haber-Bosch process that is limited by the Brønsted–Evans–Polanyi relation. Here, the authors propose a new strategy that an anchored Fe3 on θ-Al2O3(010) surface serves as a heterogeneous single cluster catalyst for ammonia synthesis from first-principles calculations and microkinetic analysis.

    • Jin-Cheng Liu
    • , Xue-Lu Ma
    •  & Jun Li

  • Article
    | Open Access

    Controlling complex photoresponsive systems while minimizing light input is highly challenging. Here, the authors report two photoswitchable molecular tweezers responding to the same light signals with opposite changes in their binding affinities towards a guest molecule allowing for its “light-economic” relocation.

    • Sandra Wiedbrauk
    • , Thomas Bartelmann
    •  & Henry Dube

  • Article
    | Open Access

    Despite being essential to organic chemistry, the curly arrow notation of reaction mechanisms has been treated with suspicion due to its unclear connection with quantum mechanics. Here, the authors show that analysis of wavefunction 'tiles' along a reaction coordinate reveals the electron motion depicted by curly arrows.

    • Yu Liu
    • , Philip Kilby
    •  & Timothy W. Schmidt

  • 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

    The equilibrium structures and dynamics of a nanoscale system are regulated by a complex potential energy surface (PES), a key target of theoretical calculations but experimentally elusive. Here, the authors report the measurement of a key PES parameter for size-selected Au nanoclusters soft-landed on amorphous silicon nitride supports.

    • D. M. Foster
    • , R. Ferrando
    •  & R. E. Palmer

  • 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

    The catalytic activity of dioxygenase AsqJ is strictly relying on the methylation of quinolone substrates. Here, the authors apply molecular simulations, X-ray crystallography and in vitro biochemical studies to the engineering of dioxygenase AsqJ with improved catalytic activity for modified non-methylated surrogates.

    • Sophie L. Mader
    • , Alois Bräuer
    •  & Ville R. I. Kaila

  • Article
    | Open Access

    Helium was long thought to be unable to form stable solid compounds, until a recent discovery that helium reacts with sodium at high pressure. Here, the authors demonstrate the driving force for helium reactivity, showing that it can form new compounds under pressure without forming any local chemical bonds.

    • Zhen Liu
    • , Jorge Botana
    •  & Mao-sheng Miao

  • Article
    | Open Access

    Scalable graphene production from graphite via an intercalation-oxidation-reduction process is still hampered by low reproducibility and many lattice defects. Here, the authors show that reducing molecular friction by using highly crystalline graphite and mild oxidizing conditions is the key to high quality graphene.

    • Steffen Seiler
    • , Christian E. Halbig
    •  & Siegfried Eigler

  • 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 role of the 5f and 6d orbitals in the chemical bonding of the actinide elements remains debated. Here, the authors synthesize and study a tetranuclear protactinium peroxo cluster and demonstrate that protactinium represents an intersection of actinide (5f) and transition metal (6d) chemistries.

    • Richard E. Wilson
    • , Stephanie De Sio
    •  & Valérie Vallet

  • Article
    | Open Access

    The sergeants-and-soldiers effect, in which a few chiral units induce chirality in a large number of achiral molecules, is difficult to quantify at the molecular level. Here, the authors devise an elegant strategy—combining theory and a system of pure organic polyhedra with chiral and achiral vertices—to understand the mechanism of chiral amplification in discrete molecular assemblies.

    • Yu Wang
    • , Hongxun Fang
    •  & Xiaoyu Cao

  • Article
    | Open Access

    A unified framework to understand gene expression noise is still lacking. Here the authors derive a universal theorem relating the biological noise with dynamics of birth and death processes and present a model of transcription dynamics, allowing analytical prediction of the dependence of mRNA noise on mRNA lifetime variability.

    • Seong Jun Park
    • , Sanggeun Song
    •  & Jaeyoung Sung

  • 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

    Extracting kinetic models from high-throughput molecular dynamics (MD) simulations is laborious and prone to human error. Here the authors introduce a deep learning framework that automates construction of Markov state models from MD simulation data.

    • Andreas Mardt
    • , Luca Pasquali
    •  & Frank Noé

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