Theoretical chemistry articles within Nature Communications

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  • Article
    | Open Access

    Heterogeneous nucleation is a process that mediates the birth of many crystalline materials, but is not fully understood. Here, the authors show that the study of precritical cluster fluctuations paves new ways for the identification of polymorphism, polymorphic control and theoretical modeling.

    • Martin Fitzner
    • , Gabriele C. Sosso
    •  & Angelos Michaelides

  • Article
    | Open Access

    Local hydration structures at solid-liquid interfaces are important in catalytic, electrochemical, and biological processes. Here, the authors demonstrate atomic-scale 3D hydration structures around the boundary on a heterogeneous mineral surface using atomic force microscopy experiments and molecular dynamics simulations.

    • Kenichi Umeda
    • , Lidija Zivanovic
    •  & Hirofumi Yamada

  • 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

    Metal-carbon σ bonds mark the basis of organometallic chemistry, but the formation of multiple such bonds between single organic and metal entities remains a challenge. Here, the authors report a one-pot aromaticity-driven method to construct osmium-based multidentate complexes containing three metal-carbon σ bonds from multiyn chains.

    • Qingde Zhuo
    • , Jianfeng Lin
    •  & Haiping Xia

  • Article
    | Open Access

    Knowledge of the energy transfer pathways in transition metal dichalcogenides is essential to design efficient optoelectronic devices. Here, the authors use megaelectronvolt ultrafast electron diffraction to unveil the sub-picosecond lattice dynamics in MoSe2 following photoexcitation of charge carriers

    • Ming-Fu Lin
    • , Vidya Kochat
    •  & Uwe Bergmann

  • 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

    Cationic metal-organic frameworks provide promising opportunities to capture anionic pollutants, but stable frameworks with sufficiently large pores are lacking. Here the authors present a thorium-based mesoporous, cationic and hydrolytically-stable MOF that can rapidly trap inorganic and organic anionic pollutants.

    • Yuxiang Li
    • , Zaixing Yang
    •  & Shuao Wang

  • 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

    The timescale of isomerization in molecules involving ultrafast migration of constituent atoms is difficult to measure. Here the authors report that sub-100 fs isomerization time on acetylene dication in lower electronic states is not possible and point to misinterpretation of recent experimental results.

    • Zheng Li
    • , Ludger Inhester
    •  & Todd J. Martinez

  • Article
    | Open Access

    Carotenoids harvest energy from light and transfer it to chlorophylls during photosynthesis. Here, Feng et al. perform ab initio calculations on excited-state dynamics and simulated 2D electronic spectrum of carotenoids, supporting the existence of a new excited state in carotenoids.

    • Jin Feng
    • , Chi-Wei Tseng
    •  & Yuchen Ma

  • Article
    | Open Access

    The thermodynamic stability of atomically precise, liganded metal nanoclusters remains poorly understood. Here, the authors use first-principles calculations to derive a new theory that rationalizes the stability of these nanoclusters as a function of their composition and morphology.

    • Michael G. Taylor
    •  & Giannis Mpourmpakis

  • Article
    | Open Access

    Soft solids have important applications in industry but their material properties can be compromised by aging. Here Bouzidet al. present a large-scale study of a model gel to investigate the aging of soft matter which can help unravel the microscopic dynamics in a range of soft solids.

    • Mehdi Bouzid
    • , Jader Colombo
    •  & Emanuela Del Gado

  • Article
    | Open Access

    The competition between chemical reactions critically affects our natural environment and the synthesis of new materials. Here, the authors present an approach to directly image distinct fingerprints of essential organic reactions and monitor their competition as a function of steric substitution.

    • Eduardo Carrascosa
    • , Jennifer Meyer
    •  & Roland Wester

  • 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

    Understanding ice nucleation is important for the development of accurate cloud models. Here Biet al. show that sharp wedges can enhance ice nucleation both when the wedge geometry matches the ice lattice and when such matching is absent, in which case nucleation is promoted by topological defects.

    • Yuanfei Bi
    • , Boxiao Cao
    •  & Tianshu Li

  • Article
    | Open Access

    Ice recrystallization is important for a range of research fields, both applied and fundamental, however the effect of ions on this process is not well known. Here the authors discover an ion-specific Hofmeister type effect on ice recrystallization, using this phenomenon to prepare porous materials with tuneable pore sizes.

    • Shuwang Wu
    • , Chongqin Zhu
    •  & Jianjun Wang

  • Article
    | Open Access

    Liquid crystal mixtures are used in commercial applications and their composition affects their properties. Here Rahimiet al. use atomistic simulations to show that defects influence the molecular arrangement of the mixture components leading to a deviation of the local order from that of the bulk.

    • Mohammad Rahimi
    • , Hadi Ramezani-Dakhel
    •  & Juan J. de Pablo

  • Article
    | Open Access

    Controlling the self-assembly of oligothiophene complexes that are used in multi-functional thin films can be challenging. Here the authors show a hierarchy of non-covalent interactions for robust self-assembly that orders Saturn-like complexes of fullerenes with oligothiophene macrocycles.

    • José D. Cojal González
    • , Masahiko Iyoda
    •  & Jürgen P. Rabe

  • Article
    | Open Access

    Finding catalyst mechanisms remains a challenge due to the complexity of hydrocarbon chemistry. Here, the authors shows that scaling relations and machine-learning methods can focus full-accuracy methods on the small subset of rate-limiting reactions allowing larger reaction networks to be treated.

    • Zachary W. Ulissi
    • , Andrew J. Medford
    •  & Jens K. Nørskov

  • Article
    | Open Access

    Manipulating chemical reactions using laser pulses to control electron transfer is an attractive goal, however much of the underlying physics remains unexplored. Here the authors analyse and explain the intramolecular electronic transfer occurring during charge-separation in acetylene, a model donor-bridge-acceptor molecule.

    • Xunmo Yang
    • , Theo Keane
    •  & Eric R. Bittner

  • Article
    | Open Access

    Natural supplies of bryostatin, a compound in clinical trials for Alzheimer’s disease, cancer, and HIV, are scarce. Here, the authors perform molecular dynamics simulations to understand how bryostatin interacts with membrane-bound protein kinase C, offering insights for the design of bryostatin analogs.

    • Steven M. Ryckbosch
    • , Paul A. Wender
    •  & Vijay S. Pande

  • Article
    | Open Access

    The nitrate anion, NO3−, is typically thought of as an electron-donating molecular moiety. Here the authors reveal, however, that when the negative charge on NO3−is smeared out over a large enough area, a positive potential emerges on N that can act as a Lewis acid in the solid state.

    • Antonio Bauzá
    • , Antonio Frontera
    •  & Tiddo J. Mooibroek

  • Article
    | Open Access

    G-protein-coupled receptors trigger several signalling pathways and their activity was proposed to be allosteric modulated by cholesterol. Here the authors use molecular dynamics simulations and ligand binding assays to show that membrane cholesterol can bind to adenosine A2Areceptor orthosteric site.

    • Ramon Guixà-González
    • , José L. Albasanz
    •  & Jana Selent

  • Article
    | Open Access

    Attractive, non-covalent interactions between aromatic rings—termedπ−πstacking—is common in chemistry but difficult to model. Here the authors report a quantum-mechanical model to show the importance of collective charge fluctuations for understanding pi-stacked supramolecular systems.

    • Jan Hermann
    • , Dario Alfè
    •  & Alexandre Tkatchenko

  • Article
    | Open Access

    High-valent iron compounds do not form spontaneously under ambient conditions and those that are synthetically available are rarely stable. Here, the authors synthesize stable iron(IV) hexahydrazide clathrochelate complexes in aqueous media via a metal-templated reaction accompanied by aerobic oxidation.

    • Stefania Tomyn
    • , Sergii I. Shylin
    •  & Igor O. Fritsky

  • Article
    | Open Access

    It is commonly held that van der Waals wells are inevitable in chemical reactions. Here, the authors show that weak van der Waals forces in the entrance channel of a prototypical complex-forming reaction cause a van der Waals saddle instead, with different dynamical effects from a well at low collision energies.

    • Zhitao Shen
    • , Haitao Ma
    •  & Jianwei Cao

  • 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

    Polymorph selection by synthesis conditions is common, important and mechanistically undercharacterized. Here authors show viaab initio calculations that surface energy effects on nucleation rate can explain how solution pH selects dominant forms of FeS2during hydrothermal synthesis.

    • Daniil A. Kitchaev
    •  & Gerbrand Ceder

  • Article
    | Open Access

    Antimicrobial peptides (AMPs) selectively form pores in microbial membranes in process not fully understood. Here the authors use experimentally guided molecular dynamics to study maculatin pore formation, showing how this AMP assembles into transient and structurally diverse oligomeric pores in cell membranes.

    • Yukun Wang
    • , Charles H. Chen
    •  & Jakob P. Ulmschneider

  • Article
    | Open Access

    Propensity for a given Λ-doublet level is a common feature in many chemical reactions, but has so far remained unexplained. Here, the authors show how to predict computationally those propensities and relate them to the reaction mechanism on concurrent potential energy surfaces.

    • P. G. Jambrina
    • , A. Zanchet
    •  & F. J. Aoiz

  • 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 organization of supramolecular peptide polymers determines their properties; however, controlling their dimensions still remains a problem. Here, Gazitet al. show the spontaneous elongation and shortening of these polymers at an individual nano-assembly level by using a microfluidic platform.

    • Zohar A. Arnon
    • , Andreas Vitalis
    •  & Ehud Gazit

  • Article
    | Open Access

    The suppression of crystallization due to the appearance of structures with fivefold symmetry is widely adopted, but its kinetic and thermodynamic origin remains elusive. Taffs et al.show that fivefold symmetry substantially slows down the nucleation rate but not the crystal growth rate as expected.

    • Jade Taffs
    •  & C. Patrick Royall

  • Article
    | Open Access

    The high observed abundance of atmospheric methanol over remote oceans is still not well-explained. Here the authors use quantum calculations and atmospheric modelling to show the reaction of methyl peroxy and hydroxyl radicals is a major methanol source (115 Tg/yr), comparable to global terrestrial emissions.

    • Jean-François Müller
    • , Zhen Liu
    •  & Jozef Peeters

  • 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

  • Article
    | Open Access

    Sulfur-substituted nucleobases are promising photo- and chemotherapeutic drugs. Here, the authors unravel the electronic and structural aspects that lead to the ultrafast population of triplet states in these molecules, providing an explanation for their efficiency as photosensitizers.

    • Sebastian Mai
    • , Marvin Pollum
    •  & Leticia González

  • Article
    | Open Access

    Exciton coupling between organic dyes is important for opto-electronic and photovoltaic devices and it is well-known that strong coupling occurs between equal chromophores. Here, Würthner and others show quadruple dye stacks that have strong exciton coupling between different chromophores within a heteroaggregate.

    • David Bialas
    • , André Zitzler-Kunkel
    •  & Frank Würthner

  • Article
    | Open Access

    Tetrameric cationic channels specificity is determined by the sequence and structural conformation of their selectivity filter. Here, the authors show that a cationic channel from Tsukamurella paurometabola is non-selective due to a Ca2+-binding motif within its unusual proline-rich filter.

    • Balasundaresan Dhakshnamoorthy
    • , Ahmed Rohaim
    •  & Benoît Roux

  • Article
    | Open Access

    Thermal management is important for designing bio-nano interfaces for biosensing and thermotherapic applications. Here the authors perform simulations showing that nm-thick water layers between graphene and cell membranes display layered ordering, promoting interfacial thermal coupling and thermal dissipation.

    • Yanlei Wang
    • , Zhao Qin
    •  & Zhiping Xu

  • Article
    | Open Access

    It is essential to understand the effect of molecular vibration on charge transport for better design of molecular electronics. Here, the authors test two benchmark aromatic motifs and show how the coupling between π electrons and molecular vibration is affected by molecular edge topology.

    • Héctor Álvaro Galué
    • , Jos Oomens
    •  & Britta Redlich

  • Article
    | Open Access

    Density functional theory is widely used throughout the chemical sciences, but suffers from over-emphasis on charge delocalisation. Here, the authors experimentally probe the energies of two states of a diamine cation and show how a self-interaction correction allows for the accurate prediction of both states.

    • Xinxin Cheng
    • , Yao Zhang
    •  & Peter M. Weber

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