Theoretical chemistry articles within Nature Communications

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  • Article
    | Open Access

    Machine learning models insufficient for certain screening tasks can still provide valuable predictions in specific sub-domains of the considered materials. Here, the authors introduce a diagnostic tool to detect regions of low expected model error as demonstrated for the case of transparent conducting oxides.

    • Christopher Sutton
    • , Mario Boley
    •  & Matthias Scheffler

  • Article
    | Open Access

    Supercooled liquids near the glass transition show remarkable non-Arrhenius transport phenomena, whose origin is yet to be clarified. Here, the authors use GPU molecular dynamics simulations for various binary mixtures in the supercooled regime to show the validity of a quasiuniversal excess-entropy scaling relation for viscosity and diffusion.

    • Ian H. Bell
    • , Jeppe C. Dyre
    •  & Trond S. Ingebrigtsen

  • Article
    | Open Access

    Electrocatalytic water oxidation is facilitated by high valence states, but these are challenging to achieve at low applied potentials. Here, authors report a multicomponent FeCoCrNi alloy with dynamically formed Ni4+ species to offer high catalytic activity via lattice oxygen activation mechanism.

    • Ning Zhang
    • , Xiaobin Feng
    •  & Yang Chai

  • Article
    | Open Access

    The geometric phase effect associated with a conical intersection between the ground and first excited electronic state has been predicted in the H3 system below the conical intersection energy. The authors, by a crossed molecular beam technique and quantum dynamic calculations, provide experimental evidence and insight into its origin.

    • Daofu Yuan
    • , Yin Huang
    •  & Xueming Yang

  • Article
    | Open Access

    Extracting experimental operations for chemical synthesis from procedures reported in prose is a tedious task. Here the authors develop a deep-learning model based on the transformer architecture to translate experimental procedures from the field of organic chemistry into synthesis actions.

    • Alain C. Vaucher
    • , Federico Zipoli
    •  & Teodoro Laino

  • Article
    | Open Access

    Increasing the non-locality of the exchange and correlation functional in DFT theory comes at a steep increase in computational cost. Here, the authors develop NeuralXC, a supervised machine learning approach to generate density functionals close to coupled-cluster level of accuracy yet computationally efficient.

    • Sebastian Dick
    •  & Marivi Fernandez-Serra

  • Article
    | Open Access

    The polyhedral skeletal electron pair theory (PESPT), also known as Wade-Mingos’ rules, defines a relationship between skeletal bonding electron pairs and structure of clusters. Here the authors report the synthesis, structure and computational studies of planar C2B4R4 carboranes that do not adhere to PESPT.

    • Wei Lu
    • , Dinh Cao Huan Do
    •  & Rei Kinjo

  • Article
    | Open Access

    The discovery of atomically precise metal nanoclusters is generally unpredictable, and there are few examples of their rational synthesis. Here, the authors report the de novo design of Au36(SR)24 nanoclusters, from theoretical prediction to experimental synthesis and characterization of physicochemical properties.

    • Xu Liu
    • , Wen Wu Xu
    •  & Yan Zhu

  • Article
    | Open Access

    Mitochondrial apoptosis is controlled by BCL2 family proteins, and the BH3-only proteins often act as sensors that transmit apoptotic signals. Here the authors show how the BH3-only proteins BMF and HRK can directly activate the BCL2 protein BAK and interact with BAK through an alternative binding groove.

    • Kaiqin Ye
    • , Wei X. Meng
    •  & Haiming Dai

  • Article
    | Open Access

    Current models of halogen bonding describe the σ-symmetric component of this interaction but do not contemplate the possibility of π-covalency. Here the authors provide experimental and computational evidence of π-covalency in halogen bonds involving radical cation halogen bond donors.

    • Cameron W. Kellett
    • , Pierre Kennepohl
    •  & Curtis P. Berlinguette

  • Article
    | Open Access

    The choice of molecular representations can severely impact the performances of machine-learning methods. Here the authors demonstrate a persistence homology based molecular representation through an active-learning approach for predicting CO2/N2 interaction energies at the density functional theory (DFT) level.

    • Jacob Townsend
    • , Cassie Putman Micucci
    •  & Konstantinos D. Vogiatzis

  • Article
    | Open Access

    Salts in water at extreme conditions play a fundamental role in determining the properties of the Earthʼs mantle constituents. Here the authors shed light on ion-water and ion-ion interactions for NaCl dissolved in water at conditions relevant to the Earthʼs upper mantle by molecular dynamics simulations.

    • Cunzhi Zhang
    • , Federico Giberti
    •  & Giulia Galli

  • Article
    | Open Access

    Protein-ligand unbinding processes are out of reach for atomistic simulations due to time-scale involved. Here the authors demonstrate an approach relying on dissipation-corrected targeted molecular dynamics that enables to provide binding and unbinding rates with a speed-up of several orders of magnitude.

    • Steffen Wolf
    • , Benjamin Lickert
    •  & Gerhard Stock

  • Article
    | Open Access

    Dioxolenium ion intermediates formed from remote positions are hypothesized to direct stereoselective glycosylations. Herein we combine infrared ion spectroscopy, DFT calculations and synthetic work to characterize and study these dioxolenium ions and their role in stereoselective glycosylation reactions.

    • Thomas Hansen
    • , Hidde Elferink
    •  & Thomas J. Boltje

  • Article
    | Open Access

    Enzymes from organisms inhabiting cold environments (psychrophiles) have adapted to catalyzing chemical reactions at near freezing temperatures. Here – using molecular dynamics simulations – the authors analyze cold adaptation of psychrophilic α-amylase and provide the structural basis for its low anomalous temperature optimum: the increased mobility of a surface loop involved in substrate interaction.

    • Jaka Sočan
    • , Miha Purg
    •  & Johan Åqvist

  • Article
    | Open Access

    The surrounding environment’s influence on the Kondo states formed around an adsorbed transition metal atom are challenging potential applications. Here, the authors demonstrate, via STM and DFT+HEOM calculations, that a metal phthalocyanine molecule on an Au(111) surface enables a fine tuning of the Kondo characteristics.

    • Xiangyang Li
    • , Liang Zhu
    •  & Jinlong Yang

  • Article
    | Open Access

    Despite the importance of neural-network quantum states, representing fermionic matter is yet to be fully achieved. Here the authors map fermionic degrees of freedom to spin ones and use neural-networks to perform electronic structure calculations on model diatomic molecules to achieve chemical accuracy.

    • Kenny Choo
    • , Antonio Mezzacapo
    •  & Giuseppe Carleo

  • Article
    | Open Access

    The formation of chiral molecules generally relies on direct chirality transfer from catalyst to products. Here, the authors report a strategy based on point chirality transfer from the catalyst to a dirhodium carbene intermediate with axial chirality, which is then transferred to products via C(sp2)-H functionalization.

    • Kuiyong Dong
    • , Xing Fan
    •  & Xinfang Xu

  • Article
    | Open Access

    Bond dissociation enthalpies are key quantities in determining chemical reactivity, their computations with quantum mechanical methods being highly demanding. Here the authors develop a machine learning approach to calculate accurate dissociation enthalpies for organic molecules with sub-second computational cost.

    • Peter C. St. John
    • , Yanfei Guan
    •  & Robert S. Paton

  • Article
    | Open Access

    Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed different ion permeation rates of MthK in membranes with different properties.

    • Ruo-Xu Gu
    •  & Bert L. de Groot

  • Article
    | Open Access

    Photoabsorption is a fundamental process that leads to changes in the electron density in matter. Here, the authors show a direct measurement of the distribution of electron density when a cyclohexadine molecule is excited by pulsed UV radiation and probed by a time delayed X-ray pulse generated at LCLS.

    • Haiwang Yong
    • , Nikola Zotev
    •  & Peter M. Weber

  • Article
    | Open Access

    The unexpectedly long-ranged interface stress observed in recent delamination experiments is yet to be clarified. Here, the authors develop an analytical approach to show the wavelike atomic deformation as the origin for the observed ultra long-range stress in delamination of graphene from various substrates.

    • Paul Hauseux
    • , Thanh-Tung Nguyen
    •  & Alexandre Tkatchenko

  • Article
    | Open Access

    The experimental observation that water dimers diffuse more rapidly than monomers across materials’ surfaces is yet to be clarified. Here the authors show by ab initio calculations classical and quantum mechanical mechanisms for faster water dimer diffusion on a broad range of metal and non-metal surfaces.

    • Wei Fang
    • , Ji Chen
    •  & Angelos Michaelides

  • Article
    | Open Access

    Graphene oxide holds great promise for water purification applications, though its chemical reactivity in water is yet to be clarified. Here the authors show by first principles molecular dynamics that graphene oxide structures with correlated functional groups and regions of pristine graphene are the most stable in liquid water.

    • Félix Mouhat
    • , François-Xavier Coudert
    •  & Marie-Laure Bocquet

  • Article
    | Open Access

    Metal-ligand δ and φ interactions, though considered weak, may be necessary for fully describing the electronic and geometric structures of certain compounds. Here, in actinide metallacycles, the authors discover two new types of M-L δ and φ back-bonds that contribute substantially to their unusual chemical behavior.

    • Morgan P. Kelley
    • , Ivan A. Popov
    •  & Ping Yang

  • 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

    Artificial molecules supported on templated surfaces attract enormous interest due to their tunable electronic properties. Here the authors use STM experiments and DFT calculations to show the formation of Pb artificial clusters on a IrTe2 honeycomb template that are maximally stabilized by relativistic effects.

    • Jae Whan Park
    • , Hyo Sung Kim
    •  & Han Woong Yeom

  • Article
    | Open Access

    The determination of the speciation of ions and molecules in supercritical aqueous fluids under pressure is key to understanding their mass transport in the Earth’s interior. Here the authors present a strategy based on ab-initio molecular dynamics to determine the speciation of carbonates in aqueous fluids.

    • Ding Pan
    •  & Giulia Galli

  • Article
    | Open Access

    Supramolecular catalytic assemblies attract enormous interest due to their activity that rivals natural enzymes. Using ab initio molecular dynamics, the authors show that a gold catalyst in a Ga4L612- nanocage, while impeded by reorganization energy, is accelerated by hosting a catalytic water molecule.

    • Valerie Vaissier Welborn
    • , Wan-Lu Li
    •  & Teresa Head-Gordon

  • Article
    | Open Access

    Feshbach resonances are transiently trapped states along a reaction coordinate, providing a probe to the reaction’s potential energy surface (PES) but difficult to analyze in polyatomic systems. Here the authors identify Feshbach resonances in a reacting 4-atom system by state-to-state quantum dynamics using a full-dimensional PES.

    • Xiaoren Zhang
    • , Lulu Li
    •  & Dong H. Zhang

  • Article
    | Open Access

    Although artificial Lieb lattices have been recently synthesized, the realization of a Lieb lattice in a real material is still challenging. Here the authors use tight-binding and first principle calculations to predict tunable topology and magnetism in recently discovered two-dimensional covalent-organic frameworks.

    • Bin Cui
    • , Xingwen Zheng
    •  & Bing Huang

  • 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

    In Suzuki coupling reactions, excellent catalytic performance require negatively charged Pd species and the avoidance of metal leaching or clustering. Here the authors implanted Pd sites into an intermetallic electride, Y3Pd2, which serves as an efficient and stable catalyst for Suzuki coupling reactions.

    • Tian-Nan Ye
    • , Yangfan Lu
    •  & Hideo Hosono

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