Theoretical chemistry articles within Nature Communications

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  • Article
    | Open Access

    No existing density functional correctly describes the properties of water across the entire phase diagram. The authors report a data-driven many-body potential energy function based on density-corrected SCAN functional that quantitatively reproduces the energetics of gas-phase water clusters, and correctly predicts the properties of liquid water.

    • Saswata Dasgupta
    • , Eleftherios Lambros
    •  & Francesco Paesani

  • Article
    | Open Access

    Layered boron compounds attract enormous interest in applications. This work reports first-principles calculations coupled with global optimization to show that the outer boron surface in MgB2 nanosheets undergo disordering and clustering, which is experimentally confirmed in synthesized MgB2 nanosheets.

    • Sichi Li
    • , Harini Gunda
    •  & Brandon C. Wood

  • Article
    | Open Access

    The present manuscript reports a Bayesian deep-learning approach for the automatic, robust classification of polycrystalline systems of both synthetic and experimental origin. The unsupervised analysis of the internal neural-network representations reveals physically understandable patterns.

    • Andreas Leitherer
    • , Angelo Ziletti
    •  & Luca M. Ghiringhelli

  • Article
    | Open Access

    Protonated water species have been the subject of numerous experimental and computational studies. Here the authors provide a nearly complete assignment of the experimental IR spectrum of the H+(H2O)21 water cluster based on high-level wavefunction theory and anharmonic vibrational quasi-degenerate perturbation theory.

    • Jinfeng Liu
    • , Jinrong Yang
    •  & Xiao He

  • Article
    | Open Access

    Experimental determination of new cocrystals remains challenging due to the need of a systematic screening with a large range of coformers. Here the authors develop a flexible deep learning framework based on graph neural network demonstrated to quickly predict the formation of co-crystals.

    • Yuanyuan Jiang
    • , Zongwei Yang
    •  & Xuemei Pu

  • Article
    | Open Access

    Achieving ultra-low friction at macroscopic scales is highly desirable. In this work molecular dynamics simulations of graphitic contacts incorporating corrugated grain boundaries reveal an unusual non-monotonic variation of friction with normal load and temperature due to dynamic buckling effects.

    • Xiang Gao
    • , Wengen Ouyang
    •  & Oded Hod

  • Article
    | Open Access

    Aqueous solutions under nanoscale confinement exhibit interesting physicochemical properties. This work reports evidence on the spontaneous formation of two-dimensional alkali chloride crystalline/non-crystalline nanostructures in dilute aqueous solution under nanoscale confinement by computer simulations.

    • Wenhui Zhao
    • , Yunxiang Sun
    •  & Xiao Cheng Zeng

  • Article
    | Open Access

    High-nitrogen content polyhedral molecules are of fundamental interest for theory and for synthesis applications. The authors, using isomer selective, tunable soft photoionization reflectron time-of-flight mass spectrometry, identify the formation of a hitherto elusive prismatic P3N3 molecule during sublimation of PH3 and N2 ice mixtures exposed to energetic electrons.

    • Cheng Zhu
    • , André K. Eckhardt
    •  & Ralf I. Kaiser

  • Article
    | Open Access

    Understanding the catalysts’ structure evolution under working conditions is challenging. Here the authors use a multiscale simulation approach and machine learning to study the structures and nucleation of CeO2-supported Pd clusters and single atoms at various catalyst loadings, temperatures, and exposures to CO.

    • Yifan Wang
    • , Jake Kalscheur
    •  & Dionisios G. Vlachos

  • Article
    | Open Access

    Commonly, large π-conjugated systems facilitate low-energy electronic transitions. Here, the authors demonstrate that the relief of excited-state antiaromaticity of the benzene core leads to large Stokes shifts, and allows the construction of emitters covering the entire visible spectrum without the need of extending π-conjugation.

    • Heechan Kim
    • , Woojin Park
    •  & Dongwhan Lee

  • Article
    | Open Access

    Multistep nucleation phenomena are of considerable fundamental interest. Here the authors combine molecular dynamics, machine learning and molecular cluster analysis to investigate the multistep nucleation of smectic clusters from a nematic fluid that cannot be accounted for by the classical nucleation theory.

    • Kazuaki Z. Takahashi
    • , Takeshi Aoyagi
    •  & Jun-ichi Fukuda

  • Article
    | Open Access

    Machine learning faces challenges in catalyst design due to its black-box nature. Here, the authors develop a theory-infused neural network approach that integrates deep learning algorithms with the well-established d-band theory of chemisorption for reactivity prediction of transition-metal surfaces.

    • Shih-Han Wang
    • , Hemanth Somarajan Pillai
    •  & Hongliang Xin

  • Article
    | Open Access

    Neural Networks are known to perform poorly outside of their training domain. Here the authors propose an inverse sampling strategy to train neural network potentials enabling to drive atomistic systems towards high-likelihood and high-uncertainty configurations without the need for molecular dynamics simulations.

    • Daniel Schwalbe-Koda
    • , Aik Rui Tan
    •  & Rafael Gómez-Bombarelli

  • Article
    | Open Access

    Tetrel bonds are noncovalent interactions between electron donors and group 14 elements; in these situations, C(sp3) atoms can act as Lewis acids, accepting electron density. Here, the authors show that methyl groups, when bound to atoms less electronegative than carbon, can participate in noncovalent interactions as electron density donors.

    • Oliver Loveday
    •  & Jorge Echeverría

  • Article
    | Open Access

    Developments in the field of two-dimensional van der Waals materials offer big promise for device applications. This study reports a first-principle investigation on the dielectric properties of 32 exfoliable two-dimensional layered dieletrics for assessing the prospects of these materials in devices.

    • Mehrdad Rostami Osanloo
    • , Maarten L. Van de Put
    •  & William G. Vandenberghe

  • Article
    | Open Access

    Nematic liquid crystals with polar order bear great potential for many applications but their rational design is difficult. Mandle et al. outline a set of design principles for this new phase of matter, guided by experiments and simulation, showing polar order to be driven by steric interactions.

    • Richard J. Mandle
    • , Nerea Sebastián
    •  & Alenka Mertelj

  • Article
    | Open Access

    Quantum mechanical calculations of molecular ionized states are computationally quite expensive. This work reports a successful extension of a previous deep-neural networks approach towards transferable neural-network models for predicting multiple properties of open shell anions and cations.

    • Roman Zubatyuk
    • , Justin S. Smith
    •  & Olexandr Isayev

  • Article
    | Open Access

    The concept of delocalization, resonance and aromaticity are commonly discussed within electronic structure frameworks relying on specific wave function expansions. Here the authors propose a redefinition of these concepts from first-principles by investigating saddle points of the all-electron probability density.

    • Leonard Reuter
    •  & Arne Lüchow

  • Article
    | Open Access

    Disproportion of uranium(IV) is rare, as it is usually the stable product of uranium(III) or (V) disproportionation. Here, the authors report uranium(IV) disproportionation to uranium(III) and (V) revealing ligand and solvent control over a key thermodynamic property of uranium

    • Jingzhen Du
    • , Iskander Douair
    •  & Stephen T. Liddle

  • Article
    | Open Access

    Ternary heterometallic clusters often display intriguing structures and bonding. Here the authors prepare four [Sn2Sb5]3−-based clusters stabilized by coordination of a transition metal ion; analysis of their electronic structure reveals that the resulting cluster displays globally aromatic or antiaromatic character depending on the transition metal ion.

    • Yu-He Xu
    • , Nikolay V. Tkachenko
    •  & Zhong-Ming Sun

  • Article
    | Open Access

    Practical electrochemical N2 reduction reaction is challenged by competing side reactions. Here a combination of DFT and mikrokinetic modelling reveals the potential-dependent competition between electrochemical ammonia production and hydrogen evolution on a single-site iron catalyst embedded in N-doped graphene.

    • Changhyeok Choi
    • , Geun Ho Gu
    •  & Yousung Jung

  • Article
    | Open Access

    hNEIL1 (human endonuclease VIII-like 1) is a broadly specific DNA glycosylase for base excision repair. Here, the authors show that hNEIL1 can assume activated or triage conformations: the structural basis for the mechanism that enables broad specificity and reduces futile repair of normal bases.

    • Menghao Liu
    • , Jun Zhang
    •  & Chengqi Yi

  • Article
    | Open Access

    The conversion of N2 and CO2 into urea through electrochemical reactions under ambient conditions represents a novel green urea synthesis method. Here, the authors demonstrate that two-dimensional transition metal borides can serve as effective catalysts for electrochemical urea synthesis.

    • Xiaorong Zhu
    • , Xiaocheng Zhou
    •  & Yafei Li

  • Article
    | Open Access

    Quantum-mechanical methods of benchmark quality are widely used for describing molecular interactions. The present work shows that interaction energies by CCSD(T) and DMC are not in consistent agreement for a set of polarizable supramolecules calling for cooperative efforts solving this conundrum.

    • Yasmine S. Al-Hamdani
    • , Péter R. Nagy
    •  & Alexandre Tkatchenko

  • Article
    | Open Access

    Mechanically flexible single crystals are promising materials for advanced technological applications. Here, the authors study the high pressure response of a plastically flexible coordination polymer and provide indication of an overall disparate mechanical response of bulk flexibility and quasi-hydrostatic compression within the same crystal lattice.

    • Xiaojiao Liu
    • , Adam A. L. Michalchuk
    •  & Colin R. Pulham

  • Article
    | Open Access

    Great progress has been made in topochemistry of mobile oxygen anions, but metastable compounds have not yet been achieved by deintercalation of sulfur anions. Here, the authors prepare metastable oxychalcogenide phases by taking advantage of redox-reactive sulfur dimers embedded in a layered oxysulfide.

    • Shunsuke Sasaki
    • , Maria Teresa Caldes
    •  & Laurent Cario

  • Article
    | Open Access

    The subtle connections between water’s supercooled liquid and glassy states are difficult to characterize. Gartner et al. suggest with MD simulations that the long-range structure of glassy water may reflect signatures of water’s debated second critical point in the supercooled liquid.

    • Thomas E. Gartner III
    • , Salvatore Torquato
    •  & Pablo G. Debenedetti

  • Article
    | Open Access

    Determining the structure of amorphous solids is important for optimization of pharmaceutical formulations, but direct relation of molecular dynamics (MD) simulations and NMR to achieve this is challenging. Here, the authors use a machine learning model of chemical shifts to solve the atomic-level structure of the hydrated amorphous drug AZD5718 by combining dynamic nuclear polarization-enhanced solid-state NMR with predicted shifts for MD simulations of large systems.

    • Manuel Cordova
    • , Martins Balodis
    •  & Lyndon Emsley

  • Article
    | Open Access

    The structure of water around Brønsted acid sites in zeolites is shown to influence their catalytic activity. Here the authors shed light on confinement effects in different pores zeolites/water interfaces acidic strength by means of ab-initio molecular dynamics and enhanced sampling metadynamics techniques.

    • Emanuele Grifoni
    • , GiovanniMaria Piccini
    •  & Michele Parrinello

  • Article
    | Open Access

    Optical matter consisting of nanoparticle constituents in solution is of key interest due to the exhibited self-assembling mechanisms. The authors propose a principal components analysis based data-driven approach to determine the collective modes of colloidal clusters mimicking optical binding used in colloidal self-assembly.

    • Shiqi Chen
    • , Curtis W. Peterson
    •  & Norbert F. Scherer

  • Article
    | Open Access

    Efficient methods to calculate magnetically induced currents in metallic nanostructures are currently lacking. Here, the authors propose a theoretical method to compute and analyze magnetically induced currents in nanostructures validated for experimentally synthesized gold-based, hydrogen-containing ligand-protected clusters.

    • Omar López-Estrada
    • , Bernardo Zuniga-Gutierrez
    •  & Hannu Häkkinen

  • Article
    | Open Access

    Existing methods for organic semiconductor computational screening are limited by the computational demand of the process, leading to the identification of non-optimal material candidates. Here, the authors report machine learning method to guide the discovery of organic semiconductors.

    • Christian Kunkel
    • , Johannes T. Margraf
    •  & Karsten Reuter

  • Comment
    | Open Access

    Precise knowledge of chemical composition and atomic structure of functional nanosized systems, such as metal clusters stabilized by an organic molecular layer, allows for detailed computational work to investigate structure-property relations. Here, we discuss selected recent examples of computational work that has advanced understanding of how these clusters work in catalysis, how they interact with biological systems, and how they can make self-assembled, macroscopic materials. A growing challenge is to develop effective new simulation methods that take into account the cluster-environment interactions. These new hybrid methods are likely to contain components from electronic structure theory combined with machine learning algorithms for accelerated evaluations of atom-atom interactions.

    • Sami Malola
    •  & Hannu Häkkinen

  • Article
    | Open Access

    Engineering efforts have focused on acyltransferase (AT) domains of modular polyketide synthases (PKSs) to site-selectively modify the resulting polyketides, but critical AT residues involved in substrate selection have not been fully elucidated. Here, the authors use molecular dynamics to pinpoint mutations that impact AT domain selectivity and exchange structural motifs to obtain chimeric PKS modules with expanded substrate specificity.

    • Edward Kalkreuter
    • , Kyle S. Bingham
    •  & Gavin J. Williams

  • Article
    | Open Access

    Pauling’s electronegativity scale has a fundamental value and uses accessible thermochemical data, but fails at predicting the bonding behavior for several elements. The authors propose their thermochemical scale based on experimental dissociation energies that provides dimensionless values for the electronegativity and recovers the correct trends throughout the periodic table.

    • Christian Tantardini
    •  & Artem R. Oganov

  • Article
    | Open Access

    Electrocatalytic conversion of nitrogen oxides to value-added chemicals is a promising strategy for mitigating the imbalance in the global nitrogen cycle. Here, the authors present iron–nitrogen-doped carbon as an efficient and durable electrocatalyst for selective nitric oxide reduction to hydroxylamine.

    • Dong Hyun Kim
    • , Stefan Ringe
    •  & Chang Hyuck Choi

  • Article
    | Open Access

    The relationship between the strain rate and micro-scale deformation in metals is still poorly understood. Here the authors use discrete dislocation dynamics and molecular dynamics to establish a universal relationship between material strength, dislocation density, strain rate and dislocation mobility in fcc metals.

    • Haidong Fan
    • , Qingyuan Wang
    •  & Michael Zaiser

  • Article
    | Open Access

    Single-atom metal alloys attract considerable interest as alternative metal hydrogenation catalysts. Here the authors combine first-principles calculations with compressed-sensing data-analytics approaches to develop stability and activity’s descriptors for screening single atom alloy catalysts.

    • Zhong-Kang Han
    • , Debalaya Sarker
    •  & Sergey V. Levchenko

  • Article
    | Open Access

    Controlling the electronic states of molecules is a fundamental challenge for future sub-nanoscale device technologies but the external dynamical control of these states still awaits experimental realization. Here, via quantum chemical calculations, the authors demonstrate that in-plane uniaxial strain of 2D covalently linked arrays of radical units induces controlled pairing of π-conjugated electrons in a reversible way.

    • Isaac Alcón
    • , Raúl Santiago
    •  & Stefan T. Bromley

  • Article
    | Open Access

    Machine learning algorithms offer new possibilities for automating reaction procedures. The present paper investigates automated reaction’s prediction with Molecular Transformer, the state-of-the-art model for reaction prediction, proposing a new debiased dataset for a realistic assessment of the model’s performance.

    • Dávid Péter Kovács
    • , William McCorkindale
    •  & Alpha A. Lee

  • Article
    | Open Access

    Connecting conformational dynamics and epistasis has so far been limited to a few proteins and a single fitness trait. Here, the authors provide evidence of positive epistasis on multiple catalytic traits in the evolution and dynamics of engineered cytochrome P450 monooxygenase, offering insights for in silico protein design.

    • Carlos G. Acevedo-Rocha
    • , Aitao Li
    •  & Manfred T. Reetz

  • Article
    | Open Access

    Bicyclo[1.1.1]pentanes (BCPs) are important motifs in contemporary drug design, however, approaches to BCPs featuring adjacent stereocenters are rather limited. Here, the authors report a photo- and organocatalyzed asymmetric addition of simple aldehydes to [1.1.1]propellane to generate enantioenriched α-chiral BCPs.

    • Marie L. J. Wong
    • , Alistair J. Sterling
    •  & Edward A. Anderson

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