Reaction kinetics and dynamics articles within Nature Communications

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  • Article
    | Open Access

    Despite the importance of dynamic phosphorylation in biology, enzyme-free, synthetic systems that use dynamic phosphorylation to regulate supramolecular processes are unexplored. Here, the authors report an enzyme-free chemical reaction cycle that can dynamically phosphorylate amino acids and peptides using simple phosphorylating agents and regulate supramolecular functions.

    • Simone M. Poprawa
    • , Michele Stasi
    •  & Job Boekhoven

  • Article
    | Open Access

    Enzymes involve structural flexibility in their function, but understanding enzyme catalysis as connected to protein motions is a major challenge. Here, the authors obtain energetic description of C-H activation in nicotinamide coenzyme-dependent UDP-glucuronic acid C4 epimerase based on temperature kinetic studies and isotope effect measurements.

    • Christian Rapp
    • , Annika Borg
    •  & Bernd Nidetzky

  • Article
    | Open Access

    Experimental characterization of the transition state in chemical reactions is challenging due to its transient nature. Here, Zhang et al. observe quantum states near the activated complex region of the F + NH3 → HF + NH2 reaction via a dipole-bound state of the FNH3- anion formed upon photodetachment, which allows probing regions of reactive potential energy surfaces out of the Franck-Condon-active areas.

    • Rui Zhang
    • , Shuaiting Yan
    •  & Chuangang Ning

  • Article
    | Open Access

    Multiple autocatalytic reactions producing thiols are known, but negative feedback loop motifs are unavailable for thiol chemistry. Here, the authors develop a negative feedback loop based on the selenocarbonates, in which thiols induce the release of aromatic selenols that catalyze the oxidation of thiols by organic peroxides.

    • Xiuxiu Li
    • , Polina Fomitskaya
    •  & Sergey N. Semenov

  • Article
    | Open Access

    Radicals are expected to be inactive on metal surfaces. Here the authors describe general intermolecular radical transfer reactions on Ag and Cu surfaces and confirm the reaction mechanism by extensive control experiments.

    • Junbo Wang
    • , Kaifeng Niu
    •  & Lifeng Chi

  • Article
    | Open Access

    Aqueous batteries have a short lifespan due to Al current collector corrosion and Li loss from side reactions on the anode. Here, the authors propose a prototype of self-prolonging aqueous Li-ion batteries by introducing hydrolyzation-type anodic additives to regulate Al corrosion-passivation.

    • Binghang Liu
    • , Tianshi Lv
    •  & Liumin Suo

  • Article
    | Open Access

    The formation of C–H bonds via reaction of small inorganic molecules is of great interest for understanding the transition from inorganic to organic matter, but the detailed mechanisms remain elusive. Here, the authors demonstrate real-time visualization and coherent control of the ultrafast C–H bond formation dynamics in a light-induced bimolecular reaction from inorganic species.

    • Zhejun Jiang
    • , Hao Huang
    •  & Jian Wu

  • Article
    | Open Access

    Amyloid fibrils are ordered protein assemblies implicated in neurodegenerative disease. Here the authors show that hairpin trimers can be transition states of fibril nucleation, explaining how different fibril isoforms may arise from alternative nucleation sites.

    • Levent Sari
    • , Sofia Bali
    •  & Milo M. Lin

  • Article
    | Open Access

    The interconversion of the two spin isomers of formaldehyd has been studied in the gas phase but has never been observed experimentally in the condensed phase. Here the authors report the encapsulation of formaldehyde inside C60 cages and observe spin-isomer conversion of the formaldehyde guest molecules in the cryogenic solid state.

    • Vijyesh K. Vyas
    • , George R. Bacanu
    •  & Richard J. Whitby

  • Article
    | Open Access

    The charge-transfer reaction Ar++N2 → Ar+N2+ has been largely studied as a model gas-phase reaction but many aspects remain to be understood. Here, differential cross sections of the reaction are measured and calculated with Ar+ prepared in 2P1/2 state, showing that the charge-transfer dynamics differs significantly for Ar+(2P1/2) compared to Ar+(2P3/2) when colliding with N2.

    • Guodong Zhang
    • , Dandan Lu
    •  & Hong Gao

  • Article
    | Open Access

    Here the authors combine 19 F NMR and femtosecond transient absorption to characterise the structural origin of the multiphasic quenching dynamics in various species of BLUF domains, highlighting the importance of the heterogeneous active-site H-bond network.

    • Yalin Zhou
    • , Siwei Tang
    •  & Dongping Zhong

  • Article
    | Open Access

    Hydrated electrons at the water/air interface participate in natural and synthetic processes, but investigation of their properties remains challenging. Here the authors show that most of their electron density is solvated below the dividing surface and solvates into the bulk in around 10 picoseconds, leaving its phenoxyl radical source at the interface.

    • Caleb J. C. Jordan
    • , Marc P. Coons
    •  & Jan R. R. Verlet

  • Article
    | Open Access

    Coacervate droplets are promising protocells that sequester nutrients, but how new peptides could be synthesized inside coacervates remains a mystery. Here, the authors develop redox-active coacervates that facilitate the formation of new peptide bonds.

    • Jiahua Wang
    • , Manzar Abbas
    •  & Evan Spruijt

  • Article
    | Open Access

    The nucleation of calcium silicate hydrate is a crucial step in cement hydration, but is still a poorly understood process. Here the authors use atomistic simulations to study primary particles and their aggregation, revealing a potential C-S-H “basic building block”.

    • Xabier M. Aretxabaleta
    • , Jon López-Zorrilla
    •  & Hegoi Manzano

  • Article
    | Open Access

    Understanding the activity and selectivity of metal catalysts requires elucidating the dynamics of CO2•− radicals bound to the surface. Here, the authors use pulse radiolysis to directly observe the stabilization process of CO2•− radicals at nanoscale metallic sites from nanoseconds to seconds.

    • Zhiwen Jiang
    • , Carine Clavaguéra
    •  & Mehran Mostafavi

  • Article
    | Open Access

    The mechanisms by which changes in local geometries of receptor sites lower activation reaction barriers in electronically uncoupled, remote reaction moieties remain relatively unexplored. Here, the authors demonstrate allosteric acceleration in the thermal isomerization of an alkene triggered by the binding of a metal ion to a remote receptor site.

    • Yichen Yu
    • , Robert T. O’Neill
    •  & Stephen L. Craig

  • Article
    | Open Access

    The oxidation of aromatics contributes significantly to the formation of atmospheric aerosol. Using toluene as an example the authors demonstrate a molecular rearrangement channel in the oxidation mechanism and show that the bicyclic peroxy radicals are much less stable than previously thought and can lead to aerosol-forming low-volatility products with up to 9 oxygen atoms on sub-second timescales

    • Siddharth Iyer
    • , Avinash Kumar
    •  & Matti Rissanen

  • Article
    | Open Access

    Control of chemical reactivity through excitation of rotational states is a relatively unexplored process that may play a role in interstellar chemistry. Here the authors show a marked acceleration of the hydrogen abstraction reaction between SiO+ and H2 by exciting super-rotor states of SiO+, in a joint experimental and theoretical study.

    • Sruthi Venkataramanababu
    • , Anyang Li
    •  & Brian C. Odom

  • Article
    | Open Access

    Electrocyclic reactions proceed through critical geometries, which are known as pericyclic transition states in thermal reactions and pericyclic minima in photochemical reactions. Here, the authors image the structure of a pericyclic minimum in real time using a combination of ultrafast electron diffraction and ab initio dynamics simulations.

    • Y. Liu
    • , D. M. Sanchez
    •  & T. J. A. Wolf

  • Article
    | Open Access

    Reliably identifying transient intermediates is crucial to elucidate chemical reaction mechanisms. Here, the authors use femtosecond Fe Kβ main line and valence-to-core x-ray emission spectroscopy to characterize a short-lived intermediate of the aqueous ferricyanide photo-aquation reaction.

    • Marco Reinhard
    • , Alessandro Gallo
    •  & Dimosthenis Sokaras

  • Article
    | Open Access

    Nanobowls represent building blocks of fullerenes and nanotubes as detected in combustion systems and deep space, but their formation mechanisms in these environments have remained elusive. Here, the authors explore the gas-phase formation of benzocorannulene and beyond to the C40 nanobowl.

    • Lotefa B. Tuli
    • , Shane J. Goettl
    •  & Ralf I. Kaiser

  • Article
    | Open Access

    The abundances of small Polycyclic Aromatic Hydrocarbons (PAHs) observed in interstellar clouds has surprised astronomers and confounded astrochemical models. Here, the authors show that fast radiative cooling by Recurrent Fluorescence efficiently stabilizes the small PAH cation 1-cyanonaphthalene.

    • Mark H. Stockett
    • , James N. Bull
    •  & Boxing Zhu

  • Article
    | Open Access

    Propylene and propylene oxide are formed over boron nitride or SiO2 in the gas phase without yielding large amounts of CO2. Conversion at non-specific interfaces can thus be a successful strategy for the synthesis of oxidation-sensitive products.

    • Pierre Kube
    • , Jinhu Dong
    •  & Annette Trunschke

  • Article
    | Open Access

    Experimentally following the ultrafast dynamics of microsolvated molecules is challenging due to the inherently produced soup mix of various gas-phase aggregates. Here, the authors exploit neutral-species selection to reveal intimate details of the UV-induced ultrafast dynamics in the prototypical indole-water system.

    • Jolijn Onvlee
    • , Sebastian Trippel
    •  & Jochen Küpper

  • Article
    | Open Access

    Hydrogen binding and furfural adsorption are critical steps in Pd-catalyzed furfural hydrogenation reactions in aqueous phases. Here, the authors explore how hydronium ion at different pH values modifies the rate constant for this reaction.

    • Iris K. M. Yu
    • , Fuli Deng
    •  & Johannes A. Lercher

  • Article
    | Open Access

    The reaction speed of like-charged compounds in water is extremely slow due to Coulomb repulsions. Here, the authors boost kinetics up to 5 million times by screening these interactions and increasing the local concentration of reactants using positively charged micelles. They show the effect for two independent systems and present a theoretical explanation.

    • Adam Kowalski
    • , Krzysztof Bielec
    •  & Robert Holyst

  • Article
    | Open Access

    With a combined experimental and computational study, Jin et al. demonstrate that hematite nanoparticles can efficiently degrade phthalates under ambient humidity conditions, with a rate strongly dependent on the exposed facet via bidentate coordination involving neighbor Fe atoms, suggesting their possible use for indoor air purification

    • Xin Jin
    • , Dingding Wu
    •  & Cheng Gu

  • Article
    | Open Access

    Atmosphere aerosol nucleation contributes to climate change, air pollution, and human health, however the mechanisms are complex and elusive. Here the authors propose a general workflow based on deep neural network-based force field, paving the way towards fully ab initio simulation of atmospheric aerosol nucleation.

    • Shuai Jiang
    • , Yi-Rong Liu
    •  & Wei Huang

  • Article
    | Open Access

    Determining the time evolution of reactions at the quantum mechanical level improves our understanding of molecular dynamics. Here, authors separate the breakup of water, one bond at a time, from other processes leading to the same final products and experimentally identify, separate, and follow step by step two breakup paths of the transient OD+ fragment.

    • Travis Severt
    • , Zachary L. Streeter
    •  & Itzik Ben-Itzhak

  • Article
    | Open Access

    Ziegler-type polyolefin catalysts have proven to be hard to characterize. Here the authors present a model system consisting of patterned LaOCl spherical caps, simulating bulk particles while facilitating the use of micro(-spectro)scopic characterization techniques specifically aimed at surfaces.

    • Koen W. Bossers
    • , Laurens D. B. Mandemaker
    •  & Bert M. Weckhuysen

  • Article
    | Open Access

    Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) are of significant importance in physical organic chemistry. Here, the authors show that the competing factor of E2 as opposed to steric hindrance determines the low reactivity of SN2 in the F− + (CH3)3CI reaction.

    • Xiaoxiao Lu
    • , Chenyao Shang
    •  & Dong H. Zhang

  • Article
    | Open Access

    The discovery and control of the synthesis of metal–organic frameworks remains challenging due to the lack of understanding of their nucleation and growth. Here, the authors report a detailed molecular-level mechanism of the formation of MIL-53(Al).

    • Daniil Salionov
    • , Olesya O. Semivrazhskaya
    •  & Vitaly L. Sushkevich

  • Article
    | Open Access

    Solid–liquid interfaces are ubiquitous in natural and technological processes, but their imaging at the atomic scale has been challenging. The authors, using liquid-phase transmission electron microscopy, identify a quasi-liquid phase and the mass transport between the surface of In and Sn nanocrystals and an aqueous solution.

    • Xinxing Peng
    • , Fu-Chun Zhu
    •  & Haimei Zheng

  • Article
    | Open Access

    Nitrenium ions are highly electrophilic reactive intermediates of formula R−N−R+, nitrogen analogue of carbenes. Here the authors report the detection of a triplet nitrenium ion using time-resolved spectroscopic methods and ab initio computations, allowing a glimpse at the properties and behavior of this important class of intermediates.

    • Lili Du
    • , Juanjuan Wang
    •  & Arthur H. Winter

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