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| Open AccessRoom-temperature dynamic nuclear polarization enhanced NMR spectroscopy of small biological molecules in water
Dynamic nuclear polarization (DNP) greatly improves the NMR sensitivity, but its implementation in aqueous solutions is challenging. Here the authors demonstrate carbon polarization enhancement via in situ Overhauser DNP in small biomolecules in water at room temperature and high magnetic field.
- Danhua Dai
- , Xianwei Wang
- & Jiafei Mao
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Article
| Open AccessProofreading experimentally assigned stereochemistry through Q2MM predictions in Pd-catalyzed allylic aminations
A predictive model has been created for a stereoselective palladium-catalysed allylic amination reaction. Derived only from quantum chemical data, the method is accurate enough to reveal multiple erroneous assignments in literature experiments.
- Jessica Wahlers
- , Jèssica Margalef
- & Per-Ola Norrby
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Article
| Open AccessCross-property deep transfer learning framework for enhanced predictive analytics on small materials data
Artificial intelligence and machine learning can greatly enhance materials property prediction and discovery. Here the authors propose cross-property transfer learning to build accurate models for dozens of properties with limited data availability.
- Vishu Gupta
- , Kamal Choudhary
- & Ankit Agrawal
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Article
| Open AccessA general theoretical framework to design base editors with reduced bystander effects
Base editors can edit target nucleotides, and identical ones that are within the editing window. Here the authors build an analytical model to propose general principles of editor design to reduce bystander effects.
- Qian Wang
- , Jie Yang
- & Anatoly B. Kolomeisky
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Article
| Open AccessMonovalent lanthanide(I) in borozene complexes
The most common oxidation state for lanthanides is +3. Here the authors use photoelectron spectroscopy and theoretical calculations to study half-sandwich complexes where a lanthanide center in the oxidation state +1 is bound to an aromatic wheel-like B82- ligand.
- Wan-Lu Li
- , Teng-Teng Chen
- & Lai-Sheng Wang
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Article
| Open AccessElevating density functional theory to chemical accuracy for water simulations through a density-corrected many-body formalism
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
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Article
| Open AccessSpontaneous dynamical disordering of borophenes in MgB2 and related metal borides
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
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Article
| Open AccessRobust recognition and exploratory analysis of crystal structures via Bayesian deep learning
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
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Article
| Open AccessTowards complete assignment of the infrared spectrum of the protonated water cluster H+(H2O)21
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
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Article
| Open AccessCoupling complementary strategy to flexible graph neural network for quick discovery of coformer in diverse co-crystal materials
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
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Article
| Open AccessSuperlubric polycrystalline graphene interfaces
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
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Article
| Open AccessTwo-dimensional monolayer salt nanostructures can spontaneously aggregate rather than dissolve in dilute aqueous solutions
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
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Article
| Open AccessIdentification of a prismatic P3N3 molecule formed from electron irradiated phosphine-nitrogen ices
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
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Article
| Open AccessReal-time dynamics and structures of supported subnanometer catalysts via multiscale simulations
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
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Article
| Open AccessRelief of excited-state antiaromaticity enables the smallest red emitter
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
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Article
| Open AccessMultistep nucleation of anisotropic molecules
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
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Article
| Open AccessInfusing theory into deep learning for interpretable reactivity prediction
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
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Article
| Open AccessFacile generation of bridged medium-sized polycyclic systems by rhodium-catalysed intramolecular (3+2) dipolar cycloadditions
The bridged medium-sized ring bicyclo[m.n.2] family of natural products are commonly found but difficult to synthesize efficiently. Here the authors present a cascade reaction to form the carbon skeleton, via a [3+2] cycloaddition of a captured azavinyl carbene intermediate.
- Bao-Long Hou
- , Jonathan J. Wong
- & Chuang-Chuang Li
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Article
| Open AccessControllable CO2 electrocatalytic reduction via ferroelectric switching on single atom anchored In2Se3 monolayer
Electroreduction of CO2 into chemical fuels holds promise for mitigating environmental pollution and energy crisis. This work presents a distinct design of ferroelectric catalysts with high catalytic activity and selectivity for efficient and controllable electrochemical CO2 reduction reaction.
- Lin Ju
- , Xin Tan
- & Liangzhi Kou
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Article
| Open AccessDifferentiable sampling of molecular geometries with uncertainty-based adversarial attacks
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
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Article
| Open AccessIdentification of active catalysts for the acceptorless dehydrogenation of alcohols to carbonyls
Identifying active catalysts for the conversion of alcohols into aldehydes or ketones and molecular hydrogen is highly desirable. Here the authors develop and validate against experiments a screening model based on DFT calculations and scaling relationships for identifying alcohol dehydrogenation catalysts.
- Tao Wang
- , Jin Sha
- & Carine Michel
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Article
| Open AccessMethyl groups as widespread Lewis bases in noncovalent interactions
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
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Article
| Open AccessIdentification of two-dimensional layered dielectrics from first principles
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
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Article
| Open AccessOn the molecular origins of the ferroelectric splay nematic phase
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
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Article
| Open AccessTemperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation
Classically, ice nucleation on foreign surfaces is considered a one-step process. Here, Li et al. uncover a two-barrier pathway which becomes competitive at lower temperatures, facilitated by synergistic, entropic effects of rhombic and hexagonal ice structures.
- Chu Li
- , Zhuo Liu
- & Xuhui Huang
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Article
| Open AccessTeaching a neural network to attach and detach electrons from molecules
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
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Article
| Open AccessReal space electron delocalization, resonance, and aromaticity in chemistry
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
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Article
| Open AccessEvidence for ligand- and solvent-induced disproportionation of uranium(IV)
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
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Article
| Open AccessMachine learning based energy-free structure predictions of molecules, transition states, and solids
Accurate computational prediction of atomistic structure with traditional methods is challenging. The authors report a kernel-based machine learning model capable of reconstructing 3D atomic coordinates from predicted interatomic distances across a variety of system classes.
- Dominik Lemm
- , Guido Falk von Rudorff
- & O. Anatole von Lilienfeld
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Article
| Open AccessTernary aromatic and anti-aromatic clusters derived from the hypho species [Sn2Sb5]3−
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
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Article
| Open AccessUnderstanding potential-dependent competition between electrocatalytic dinitrogen and proton reduction reactions
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
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Article
| Open AccessDNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes
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
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Article
| Open AccessElectrochemical synthesis of urea on MBenes
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
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Matters Arising
| Open AccessA double bond with weak σ- and strong π-interactions is still a double bond
- Cina Foroutan-Nejad
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Article
| Open AccessInteractions between large molecules pose a puzzle for reference quantum mechanical methods
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
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Article
| Open AccessHigh-pressure reversibility in a plastically flexible coordination polymer crystal
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
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Article
| Open AccessImproved prediction of solvation free energies by machine-learning polarizable continuum solvation model
Accurate theoretical evaluation of solvation free energy is challenging. Here the authors introduce a machine-learning based polarizable continuum solvation approach to improve the accuracy of widely accepted continuum solvation models by almost one order of magnitude without additional computational costs.
- Amin Alibakhshi
- & Bernd Hartke
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Article
| Open AccessIdentifying the key steps determining the selectivity of toluene methylation with methanol over HZSM-5
The selectivity of zeolite catalyzed toluene methylation is still under debate. Here the authors report a comprehensive theoretical investigation based on ab-initio molecular dynamics to identify the key-steps of methylation of toluene with methanol over a zeolite to produce p-xylene.
- Qingteng Chen
- , Jian Liu
- & Bo Yang
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Article
| Open AccessDesign of metastable oxychalcogenide phases by topochemical (de)intercalation of sulfur in La2O2S2
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
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Article
| Open AccessManifestations of metastable criticality in the long-range structure of model water glasses
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
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Article
| Open AccessStructure determination of an amorphous drug through large-scale NMR predictions
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
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Article
| Open AccessConfinement effects and acid strength in zeolites
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
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Article
| Open AccessData-driven reaction coordinate discovery in overdamped and non-conservative systems: application to optical matter structural isomerization
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
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Article
| Open AccessMagnetically induced currents and aromaticity in ligand-stabilized Au and AuPt superatoms
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
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Article
| Open AccessActive discovery of organic semiconductors
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
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Comment
| Open AccessProspects and challenges for computer simulations of monolayer-protected metal clusters
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
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Article
| Open AccessComputationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase
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
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Article
| Open AccessThermochemical electronegativities of the elements
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
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Article
| Open AccessSelective electrochemical reduction of nitric oxide to hydroxylamine by atomically dispersed iron catalyst
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