Article
|
Open Access
Featured
-
-
Article
| Open AccessCharge-separation driven mechanism via acylium ion intermediate migration during catalytic carbonylation in mordenite zeolite
The tremendous application of carbonylation reaction requires the elaborate explanation to reaction mechanism. Here the authors propose a charge-separation driven mechanism of methyl acetate formation via acylium ion intermediate in mordenite zeolite by an integrated reaction/diffusion kinetics model during the dimethyl ether carbonylation.
- Wei Chen
- , Karolina A. Tarach
- & Anmin Zheng
-
Article
| Open AccessRetinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin
Fluorescent proteins that self-assemble and localize in the neuron membrane are vital in neurosciences, particularly in optogenetics applications. Here the authors present a quantum-mechanics/molecular mechanics model for the photoisomerization of the natural highly fluorescent Neorhodopsin, explaining the highly fluorescent quantum yield that could lead to effective visualization of neural signals.
- Riccardo Palombo
- , Leonardo Barneschi
- & Massimo Olivucci
-
Article
| Open AccessOn the fluorescence enhancement of arch neuronal optogenetic reporters
Arch-3 rhodopsin variants are common fluorescent reporters of neuronal activity. Here, the authors show with quantum chemical modelling that a set of these proteins reveals a direct proportionality between their observed fluorescence intensity and the stability of an exotic excited-state diradical intermediate.
- Leonardo Barneschi
- , Emanuele Marsili
- & Massimo Olivucci
-
Article
| Open AccessSmall molecules targeting the disordered transactivation domain of the androgen receptor induce the formation of collapsed helical states
In this work the authors report atomically detailed computer simulations revealing the binding mechanisms of small molecule drugs to an intrinsically disordered region of the androgen receptor, a castration-resistant prostate cancer drug target.
- Jiaqi Zhu
- , Xavier Salvatella
- & Paul Robustelli
-
Article
| Open AccessTowards fully ab initio simulation of atmospheric aerosol nucleation
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 AccessNanoconfinement facilitates reactions of carbon dioxide in supercritical water
Aqueous CO2 under nanoconfinement is of great importance to the carbon storage and transport in Earth. Here, the authors apply ab initio molecular dynamics simulations to study the effects of confinement and interfaces, and show that that CO(aq) reacts more in nanoconfinement than in bulk.
- Nore Stolte
- , Rui Hou
- & Ding Pan
-
Article
| Open AccessA unifying mechanism for cation effect modulating C1 and C2 productions from CO2 electroreduction
CO2 reduction rate shows a strong dependence on alkali metal cation identity but a unified molecular picture for underlying mechanism requires further investigation. Using advanced molecular simulations and experimental kinetic studies, here the authors establish a unified mechanism for cation-coupled electron transfer.
- Seung-Jae Shin
- , Hansol Choi
- & Chang Hyuck Choi
-
Article
| Open AccessMechanism of C-N bonds formation in electrocatalytic urea production revealed by ab initio molecular dynamics simulation
Urea electrosyntehsis from CO2 and NOx is a challenging reaction that is becoming increasingly important. This work uses ab initio molecular dynamics simulations to reveal the origin of C-N coupling mechanisms and reaction networks in urea synthesis.
- Xin Liu
- , Yan Jiao
- & Shi-Zhang Qiao
-
Article
| Open AccessN-Heterocyclic carbene-based C-centered Au(I)-Ag(I) clusters with intense phosphorescence and organelle-selective translocation in cells
Photoluminescent gold clusters have unique chemical and physical properties based on their perturbed electronic structures. Here, the authors report the synthesis of carbon-centered Au(I)-Ag(I) clusters with high phosphorescence quantum yields using N-heterocyclic carbene ligands.
- Zhen Lei
- , Mizuki Endo
- & Mitsuhiko Shionoya
-
Article
| Open AccessPhotochemical and thermochemical pathways to S2 and polysulfur formation in the atmosphere of Venus
Polysulfur compounds have been ascribed as the unknown near-UV absorbers in Venusian atmosphere and play a key role in the sulfur chemical cycle of this planet. Here, authors establish their production from (SO)2 on the grounds of quantifications of photochemical and thermal pathways involved in the sulfur chemical cycle of the planet.
- Antonio Francés-Monerris
- , Javier Carmona-García
- & Daniel Roca-Sanjuán
-
Article
| Open AccessSpectral signatures of excess-proton waiting and transfer-path dynamics in aqueous hydrochloric acid solutions
The spectroscopic signatures of excess protons in HCl solutions are studied by ab initio simulations and THz experiments. Two contributions beyond the normal-mode scenario are identified that reflect proton-waiting and proton-transfer processes.
- Florian N. Brünig
- , Manuel Rammler
- & Roland R. Netz
-
Article
| Open Access3D and 2D aromatic units behave like oil and water in the case of benzocarborane derivatives
2D/2D fusion of aromatic halves leading to a global aromatic is found in many polycyclic aromatic hydrocarbons, whereas 2D/3D aromaticity is difficult to achieve. Here the authors report a computational chemistry investigation showing that 3D/2D aromatic combination is not possible.
- Jordi Poater
- , Clara Viñas
- & Francesc Teixidor
-
Article
| Open AccessChain flexibility of medicinal lipids determines their selective partitioning into lipid droplets
Lipid droplet (LD) is a highly dynamic organelle capable of regulating lipid metabolism, storage and transportation. Here, by combining molecular dynamics simulations and microbial LD engineering, the authors demonstrate that the structural flexibility of lipids is one of decisive factors in selective partitioning into LDs.
- So-Hee Son
- , Gyuri Park
- & Ju Young Lee
-
Article
| Open AccessExcited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential
The authors introduce a diabatic neural network to accelerate excitedstate, non-adiabatic simulations of azobenzene derivatives. The model predicts quantum yields for unseen species that are correlated with experiment.
- Simon Axelrod
- , Eugene Shakhnovich
- & Rafael Gómez-Bombarelli
-
Article
| Open AccessAccelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties
Screening polymer electrolytes for batteries is extremely expensive due to the complex structures and slow dynamics. Here the authors develop a machine learning scheme to accelerate the screening and explore a space much larger than past studies.
- Tian Xie
- , Arthur France-Lanord
- & Jeffrey C. Grossman
-
Article
| Open AccessThe role of references and the elusive nature of the chemical bond
The theory of chemical bonding relies on arbitrary references. Here the authors report a fundamental study on the chemical bond showing that considering the binding fragments as objects in real space enables to eliminate inherent biases.
- Ángel Martín Pendás
- & Evelio Francisco
-
Article
| Open AccessLanguage models can learn complex molecular distributions
Generative models for the novo molecular design attract enormous interest for exploring the chemical space. Here the authors investigate the application of chemical language models to challenging modeling tasks demonstrating their capability of learning complex molecular distributions.
- Daniel Flam-Shepherd
- , Kevin Zhu
- & Alán Aspuru-Guzik
-
Article
| Open AccessRhodium-catalyzed selective direct arylation of phosphines with aryl bromides
The widespread use of biaryl monophosphines is frequently hampered by the challenges associated with their modular preparation. Here, the authors report a protocol that appends arenes to arylphosphines to access a series of these compounds via rhodium-catalysed P(III)- directed ortho C–H activation, enabling one-fold, two-fold, and threefold direct arylation.
- Dingyi Wang
- , Mingjie Li
- & Zhuangzhi Shi
-
Article
| Open AccessAssessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow
The identification of active sites in cation exchanged-zeolites is computationally highly demanding. Here the authors employ a DFT-based computational framework to identify the energetically most favorable adsorption sites in any zeolite using a systematic high-throughput approach.
- Hassan A. Aljama
- , Martin Head-Gordon
- & Alexis T. Bell
-
Article
| Open AccessZeolite-confined subnanometric PtSn mimicking mortise-and-tenon joinery for catalytic propane dehydrogenation
The atomic structure of heterogeneous catalysts is usually a blackbox. Here the authors demonstrate large-scale machine learning atomic simulations help to resolve the catalyst structure and reaction mechanism of encapsulated PtSnOx clusters in zeolite that feature a mortise-and-tenon joinery structure and the superior activity towards propane dehydrogenation.
- Sicong Ma
- & Zhi-Pan Liu
-
Article
| Open AccessE(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials
An E(3)-equivariant deep learning interatomic potential is introduced for accelerating molecular dynamics simulations. The method obtains state-of-the-art accuracy, can faithfully describe dynamics of complex systems with remarkable sample efficiency.
- Simon Batzner
- , Albert Musaelian
- & Boris Kozinsky
-
Article
| Open AccessUnderstanding the rheology of nanocontacts
The rigidity of solid nanocontacts formed when metals touch is apparently lost liquidlike under large mechanical oscillations. As we show theoretically, there is no melting but oscillated nanocontacts undergo a remarkable reversible stick-slip rheology.
- Ali Khosravi
- , Antoine Lainé
- & Erio Tosatti
-
Article
| Open AccessL-tyrosine-bound ThiH structure reveals C–C bond break differences within radical SAM aromatic amino acid lyases
ThiH is a radical SAM L-tyrosine lyase involved in the biosynthesis of the thiazole ring of vitamin B1. Here, the authors report the crystal structure of ThiH in complex with its L-tyrosine substrate, revealing an unexpected protonation state and tunneling effect that lowers the reaction energy barrier.
- Patricia Amara
- , Claire Saragaglia
- & Yvain Nicolet
-
Article
| Open AccessThe stability of covalent dative bond significantly increases with increasing solvent polarity
Non covalent complexes are often considerably destabilized in the solvent. Here the authors combine vibrational Raman and NMR spectroscopy with a coupled-cluster computational investigation to show that the solvent polarity enhance the complex stability of a Me3NBH3 complex.
- Rabindranath Lo
- , Debashree Manna
- & Pavel Hobza
-
Article
| Open AccessInsights into the activity of single-atom Fe-N-C catalysts for oxygen reduction reaction
It is of high importance to understand the origin of single-atom Fe-N4 activity in oxygen reduction reaction. Here, the authors provide a model to understand the catalytic activity of Fe-N4 site from the spatial structure and energy level of the frontier orbitals by density functional theory calculations.
- Kang Liu
- , Junwei Fu
- & Min Liu
-
Article
| Open AccessCollective interactions among organometallics are exotic bonds hidden on lab shelves
The authors introduce a novel type of chemical bond termed collective bond, which is based on long-range interactions between atoms not considered to be bonded within the Lewis formalisms. Collective bonding occurs among a large family of widely used organometallics.
- Shahin Sowlati-Hashjin
- , Vojtěch Šadek
- & Cina Foroutan-Nejad
-
Article
| Open AccessPredicting the future of excitation energy transfer in light-harvesting complex with artificial intelligence-based quantum dynamics
Simulations of energy transfer in light-harvesting complexes are computationally very demanding. Here the authors apply an artificial intelligence quantum dissipative algorithm to study the excited state energy transfer dynamics in a light-harvesting complex.
- Arif Ullah
- & Pavlo O. Dral
-
Article
| Open AccessSelf-consistent determination of long-range electrostatics in neural network potentials
Machine learning-based neural network potentials often cannot describe long-range interactions. Here the authors present an approach for building neural network potentials that can describe the electronic and nuclear response of molecular systems to long-range electrostatics.
- Ang Gao
- & Richard C. Remsing
-
Article
| Open AccessAmmonia dimer: extremely fluxional but still hydrogen bonded
The long-standing question whether ammonia dimer is hydrogen bonded is solved by first-principles quantum mechanical calculations. The authors show that the dimer is extremely fluxional, but the probability of hydrogen-bonded configurations prevails.
- Jing Aling
- , Krzysztof Szalewicz
- & Ad van der Avoird
-
Article
| Open AccessMechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion
Zong and coworkers combine computational and experimental methods to decipher in detail the mechanism of action of glucuronoyl esterases, enzymes with significant biotechnological potential for decoupling lignin from polysaccharides in biomass.
- Zhiyou Zong
- , Scott Mazurkewich
- & Leila Lo Leggio
-
Article
| Open AccessMolecular orbital theory in cavity QED environments
Theoretical description of light-matter coupling in the strong-coupling regime is challenging. Here the authors introduce a fully consistent ab-initio method of molecular orbital theory applicable to material systems in quantum electrodynamics environments.
- Rosario R. Riso
- , Tor S. Haugland
- & Henrik Koch
-
Article
| Open AccessImplicitly perturbed Hamiltonian as a class of versatile and general-purpose molecular representations for machine learning
Molecular representations are fundamental tools for machine-learning models. The current work introduces a new set of molecular representations demonstrated to enable accurate predictions of molecular conformational energy and solvation free energy.
- Amin Alibakhshi
- & Bernd Hartke
-
Article
| Open AccessAb initio mechanism revealing for tricalcium silicate dissolution
Dissolution of minerals in water is ubiquitous in nature, its mechanism at the atomic level still under debate. Here, the authors investigate the dissolution mechanism of tricalcium silicate at early stage by ab initio molecular dynamics and metadynamics simulations.
- Yunjian Li
- , Hui Pan
- & Zongjin Li
-
Article
| Open AccessInverse design of 3d molecular structures with conditional generative neural networks
The targeted discovery of molecules with specific structural and chemical properties is an open challenge in computational chemistry. Here, the authors propose a conditional generative neural network for the inverse design of 3d molecular structures.
- Niklas W. A. Gebauer
- , Michael Gastegger
- & Kristof T. Schütt
-
Article
| Open AccessPhotochemistry of the pyruvate anion produces CO2, CO, CH3–, CH3, and a low energy electron
Pyruvic acid and its conjugate base, the pyruvate anion, are largely present in the atmosphere. Here the authors, using photoelectron imaging and quantum chemistry calculations, investigate the photochemistry of isolated pyruvate anions initiated by UVA radiation and report the formation of CO2, CO, and CH3− further decomposing into CH3 and a free electron.
- Connor J. Clarke
- , Jemma A. Gibbard
- & Basile F. E. Curchod
-
Article
| Open AccessAnalysis of vibronic coupling in a 4f molecular magnet with FIRMS
For molecular magnets and qubits, coupling between vibrations and electronic spins has a strong influence on spin state lifetime. Here, Kragskow et al present direct measurements of the vibronic transitions in a molecular magnet, showing the critical role of an “envelope effect” in the spectra.
- Jon G. C. Kragskow
- , Jonathan Marbey
- & Nicholas F. Chilton
-
Article
| Open AccessDissolving salt is not equivalent to applying a pressure on water
By advanced machine learning techniques, first-principles simulations find that dissolving salt in water does not change water structure drastically. It is contrary to the notion of “pressure effect” which has been widely applied over past 25 years.
- Chunyi Zhang
- , Shuwen Yue
- & Xifan Wu
-
Article
| Open AccessTailoring the coercive field in ferroelectric metal-free perovskites by hydrogen bonding
All-organic perovskites exhibit structural tunability and solution-processability, but are disadvantaged by a lower coercive field compared to inorganic ones. Here, the authors demonstrate that modulating hydrogen bond strength in such perovskites can generate a large coercive field.
- Hwa Seob Choi
- , Shunning Li
- & Kian Ping Loh
-
Article
| Open AccessOptical van-der-Waals forces in molecules: from electronic Bethe-Salpeter calculations to the many-body dispersion model
The authors devise an efficient quantum approach to address the van der Waals interactions due to photoexcitations by approximating the Bethe-Salpeter equation. Both attractive/repulsive forces can arise, that could couple to collective protein dynamics.
- Alberto Ambrosetti
- , Paolo Umari
- & Alexandre Tkatchenko
-
Article
| Open AccessUnconventional excited-state dynamics in the concerted benzyl (C7H7) radical self-reaction to anthracene (C14H10)
The reaction of benzyl radical self-reaction to anthracene opens-up a previously overlooked avenue for a more efficient synthesis of aromatic, multi-ringed structures via excited state dynamics in the gas phase.
- Ralf. I. Kaiser
- , Long Zhao
- & Alexander M. Mebel
-
Article
| Open AccessDecisive role of water and protein dynamics in residence time of p38α MAP kinase inhibitors
The molecular determinants of the residence time of a small molecule inhibitor at its target protein are not well understood. Here, Pantsar et al. show that the target protein’s conformational stability and solvent exposure are key factors governing the target residence time of kinase inhibitors.
- Tatu Pantsar
- , Philipp D. Kaiser
- & Stefan A. Laufer
-
Article
| Open AccessAmino acid gas phase circular dichroism and implications for the origin of biomolecular asymmetry
Chiroptical properties of amino acids are challenging to investigate in the gas phase due to the low vapor pressure of these molecules. Here the authors succeed in measuring circular dichroism active transitions and anisotropies in the ultraviolet range for several gas-phase amino acids, shedding light on the interactions between molecules and circularly polarized light that lead to chiral symmetry breaking.
- Cornelia Meinert
- , Adrien D. Garcia
- & Uwe J. Meierhenrich
-
Article
| Open AccessAccurate determination of solvation free energies of neutral organic compounds from first principles
Theoretical estimations of solvation free energy by continuum solvation models are generally not accurate. Here the authors report a polarizable force field fitted entirely to first-principles calculations for the estimation of free energy of solvation of arbitrary molecules.
- Leonid Pereyaslavets
- , Ganesh Kamath
- & Boris Fain
-
Article
| Open AccessArtificial-intelligence-driven discovery of catalyst genes with application to CO2 activation on semiconductor oxides
Here the authors demonstrate an artificial-intelligence based approach to identify catalytic materials features that correlate with mechanisms that trigger, facilitate, or hinder CO2 catalytic reactions.
- Aliaksei Mazheika
- , Yang-Gang Wang
- & Matthias Scheffler
-
Article
| Open AccessCan electric fields drive chemistry for an aqueous microdroplet?
Theoretical studies of the air-water interface of a water droplet show a wide distribution of strong electric fields at the surface that can make or break chemical bonds to accelerate chemical reactions over the bulk water phase.
- Hongxia Hao
- , Itai Leven
- & Teresa Head-Gordon
-
Article
| Open AccessSpookyNet: Learning force fields with electronic degrees of freedom and nonlocal effects
Current machine-learned force fields typically ignore electronic degrees of freedom. SpookyNet is a deep neural network that explicitly treats electronic degrees of freedom, closing an important remaining gap for models in quantum chemistry.
- Oliver T. Unke
- , Stefan Chmiela
- & Klaus-Robert Müller
-
Article
| Open AccessCreation of an unexpected plane of enhanced covalency in cerium(III) and berkelium(III) terpyridyl complexes
Studying how the ligand design influences the bonding of f-block complexes is crucial to control their properties. Here, the authors report the preparation of Bk(III) and Ce(III) complexes featuring a terpyridyl ligand; structural, spectroscopic, electrochemical, and theoretical analysis reveal that the ligand induces unusual bonding by creating a plane of enhanced bond covalency.
- Alyssa N. Gaiser
- , Cristian Celis-Barros
- & Thomas E. Albrecht-Schönzart
-
Article
| Open AccessA different perspective for nonphotochemical quenching in plant antenna complexes
Nonphotochemical quenching (NPQ) protects photosynthetic complexes from damage due to excess light. Here the authors explore different conformations of the plant CP29 light harvesting complex, showing how protein tuning of carotenoid excitation energies and carotenoid-chlorophyll interactions account for NPQ.
- Edoardo Cignoni
- , Margherita Lapillo
- & Benedetta Mennucci
-
Article
| Open AccessAdiabatic versus non-adiabatic electron transfer at 2D electrode materials
This combined experimental and theoretical study reveals the nature of electron transfer at graphene as grown on copper. The authors find that outer-sphere electron transfer occurs adiabatically with slower kinetics for multi- than for monolayer graphene.
- Dan-Qing Liu
- , Minkyung Kang
- & Patrick R. Unwin