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| Open AccessDeveloping a machine learning model for accurate nucleoside hydrogels prediction based on descriptors
Supramolecular nucleoside-based hydrogels have potential in biomedical applications, but there is no model to predict what nucleoside derivatives will form hydrogels. Here, the authors report a machine learning model to predict the ability of nucleoside derivatives to form hydrogels.
- Weiqi Li
- , Yinghui Wen
- & Hang Zhao
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Article
| Open AccessDynamics of the charge transfer to solvent process in aqueous iodide
Solvated electrons can be formed through photo-induced charge-transfer-to-solvent electronic states of halide ions in water. Here, the authors use machine learning accelerated molecular dynamics simulations to follow the evolution of these states for aqueous iodide in detail.
- Jinggang Lan
- , Majed Chergui
- & Alfredo Pasquarello
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Article
| Open AccessActivation and friction in enzymatic loop opening and closing dynamics
Enzymes present loops around active sites whose closing and opening dynamics are essential for its activity. Here the authors unveil the mechanism governing loop motion, showing that it involves an activated conformational rearrangement around a couple of torsional angles taking place under the strong friction exerted by the rest of loop torsions.
- Kirill Zinovjev
- , Paul Guénon
- & Iñaki Tuñón
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Article
| Open AccessTheoretical formulation of chemical equilibrium under vibrational strong coupling
Strong light-matter interactions in optical microcavities can be used to control molecular kinetic and thermodynamic phenomena. Here, the authors introduce a theory that describes the nonperturbative effects of infrared microcavities on chemical equilibria.
- Kaihong Sun
- & Raphael F. Ribeiro
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Article
| Open AccessMechanistic insight into the competition between interfacial and bulk reactions in microdroplets through N2O5 ammonolysis and hydrolysis
The authors report a computational strategy to simulate the hydrolysis and ammonolysis of N2O5 in aerosols using high-level quantum chemical methods. The computational results reveal a complete picture of the reactive uptake of N2O5 by atmospheric aerosols with or without NH3.
- Ye-Guang Fang
- , Bo Tang
- & Wei-Hai Fang
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Article
| Open AccessValence-isomer selective cycloaddition reaction of cycloheptatrienes-norcaradienes
Combining data science and organic synthesis to achieve the rapid and precise creation of complex molecules while controlling multiple selectivities is an emerging trend, but few successful examples are reported. Here, the authors develop an artificial neural network regression model using bond orbital data to predict chemical reactivities.
- Shingo Harada
- , Hiroki Takenaka
- & Tetsuhiro Nemoto
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Article
| Open AccessPrecise atom-to-atom mapping for organic reactions via human-in-the-loop machine learning
Precise atom mapping is crucial for data-driven reaction prediction, but currently lacks the required accuracy. Here, authors introduce a human-in-the-loop machine learning scheme for that purpose, and achieve high accuracy on a wide spectrum of reaction datasets.
- Shuan Chen
- , Sunggi An
- & Yousung Jung
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Article
| Open AccessRetinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct
Malakar et al. investigate the photochemical dynamics in the isomerization of bacteriorhodopsin light and dark-adapted forms and in the first photocycle intermediate, K. The results prompt a reevaluation of the counter ion model, revealing that a different protonation then that shown in the classic quadrupole so far considered must be employed to account for the experimental data.
- Partha Malakar
- , Samira Gholami
- & Sanford Ruhman
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Article
| Open AccessAqueous pyruvate partly dissociates under deep ultraviolet irradiation but is resilient to near ultraviolet excitation
The photochemistry of the pyruvate anion plays an important role in the Earth’s atmosphere and aqueous environments. Here, the authors show that excitation of aqueous pyruvate by 200 nm light leads to decarboxylation with a quantum efficiency of 20%, while excitation by 340 nm light does not cause a reaction.
- Jan Thøgersen
- , Fani Madzharova
- & Frank Jensen
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Article
| Open AccessObservation of geometric phase effect through backward angular oscillations in the H + HD → H2 + D reaction
In a combined experimental and theoretical study of the H + HD → H2 + D reaction at low collision energy (1.72 eV), the authors obtain detailed information on the quantum reaction dynamics surrounding a conical intersection.
- Shihao Li
- , Jiayu Huang
- & Xueming Yang
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Article
| Open AccessDirect in-situ insights into the asymmetric surface reconstruction of rutile TiO2 (110)
The reconstruction of rutile TiO2 (110) impacts its surface chemistry and catalytic properties. Here, the authors offer a detailed understanding of the asymmetric surface reconstruction of TiO2 (110)-(1×2) through a combination of STEM and DFT calculations.
- Wentao Yuan
- , Bingwei Chen
- & Yong Wang
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Article
| Open AccessDynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP
Understanding the molecular basis of voltage-sensing is of great importance in biology. Here, the authors use computational analysis and simulations to reveal atomic level insights into the mechanism of an isolated voltage-sensing domain.
- Spencer C. Guo
- , Rong Shen
- & Aaron R. Dinner
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Article
| Open AccessSQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes
The paper presents the universal QM-based scoring function that accurately and rapidly predicts protein-ligand binding affinities, outperforming current computational tools. This is demonstrated on the PL-REX experimental benchmark dataset.
- Adam Pecina
- , Jindřich Fanfrlík
- & Jan Řezáč
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Article
| Open AccessThe nature of carotenoid S* state and its role in the nonphotochemical quenching of plants
Plant Light Harvesting complexes adjust to light conditions via a quenching mechanism involving carotenoids. The authors use computational simulations to reveal how carotenoids’ quenching capacity is tuned by conformational changes of the complex.
- Davide Accomasso
- , Giacomo Londi
- & Benedetta Mennucci
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Article
| Open AccessVibronic effects on the quantum tunnelling of magnetisation in Kramers single-molecule magnets
Quantum tunnelling of the magnetisation limits the performance of single-molecule magnets at low temperatures. Here, the authors combine ab initio and analytical methods to show that spin-phonon coupling subtly influences tunnelling via polaron formation.
- Andrea Mattioni
- , Jakob K. Staab
- & Nicholas F. Chilton
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Article
| Open AccessDiffusion-based generative AI for exploring transition states from 2D molecular graphs
The exploration of transition state (TS) geometries is crucial for elucidating chemical reaction mechanisms and modelling their kinetics. Here, authors propose a generative AI approach to predict TS geometries just from 2D molecular graphs of a reaction.
- Seonghwan Kim
- , Jeheon Woo
- & Woo Youn Kim
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Article
| Open AccessActive machine learning model for the dynamic simulation and growth mechanisms of carbon on metal surface
Understanding the surface growth mechanism of carbon nanostructures would help designing better catalysts. Here, the authors combine active machine learning force fields with time-stamped Monte Carlo methods, to dynamically predict carbon growth on metal surfaces.
- Di Zhang
- , Peiyun Yi
- & Hao Li
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Article
| Open AccessTheory predicts 2D chiral polaritons based on achiral Fabry–Pérot cavities using apparent circular dichroism
2D chiral polaritons are light-matter states with select angular momentum holding technological promise. Here, the authors present the theory of such states, and propose their realisation based on a phenomenon called “apparent circular dichroism”.
- Andrew H. Salij
- , Randall H. Goldsmith
- & Roel Tempelaar
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Article
| Open AccessCombining stochastic resetting with Metadynamics to speed-up molecular dynamics simulations
An outstanding limitation of molecular dynamics simulations is sampling of long timescales. Here, authors combine Metadynamics, a popular enhanced sampling method, with stochastic resetting, to achieve higher speedups and improved kinetic inference.
- Ofir Blumer
- , Shlomi Reuveni
- & Barak Hirshberg
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Article
| Open AccessRydberg electron stabilizes the charge localized state of the diamine cation
Previous theoretical interpretations of the Rydberg spectra of dimethylpiperazine (DMP) debated the existence of a localized minimum on the surface of the DMP+ cation. Here, the authors show a substantial influence of the Rydberg electron on the molecular structure, restoring the localized minimum.
- Marc Reimann
- , Christoph Kirsch
- & Martin Kaupp
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Article
| Open AccessElectronic paddle-wheels in a solid-state electrolyte
Conduction in solid-state electrolytes composed of monatomic ions is found to be analogous to the paddle-wheel mechanism in molecular solid electrolytes, facilitated by rotational motion of lone pair electrons, helping unify understanding of mechanisms.
- Harender S. Dhattarwal
- , Rahul Somni
- & Richard C. Remsing
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Article
| Open AccessTowards a transferable fermionic neural wavefunction for molecules
Neural wavefunctions have become a highly accurate approach to solve the Schrödinger equation. Here, the authors propose an approach to optimize for a generalized wavefunction across compounds, which can help developing a foundation wavefunction model.
- Michael Scherbela
- , Leon Gerard
- & Philipp Grohs
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Article
| Open AccessFast free energy estimates from λ-dynamics with bias-updated Gibbs sampling
Calculations of relative binding free energy are crucial for lead optimization in structure-based drug design, but classical methods are computationally expensive. Here, the authors describe a more efficient method for calculating the free energy that is as accurate as thermodynamic integration.
- Michael T. Robo
- , Ryan L. Hayes
- & Jonah Z. Vilseck
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Article
| Open AccessElucidation of the structural basis for ligand binding and translocation in conserved insect odorant receptor co-receptors
Insects rely on olfaction for behavior control. Recent structural studies of receptors provide insight into ligand binding. Here, the authors identify dynamic binding mechanism to Orco, explaining its high selectivity with insights in compound screening.
- Jody Pacalon
- , Guillaume Audic
- & Jérémie Topin
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Article
| Open AccessAlkali metal reduction of alkali metal cations
Here the authors demonstate that counter to expectation provided by the relevant standard reduction potentials, a chloroberyllate, [{SiNDipp}BeClLi]2, reacts with the group 1 elements (M = Na, K, Rb, Cs) to provide the respective heavier alkali metal analogues, [{SiNDipp}BeClM]2.
- Kyle G. Pearce
- , Han-Ying Liu
- & Michael S. Hill
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Article
| Open AccessMulti-step nucleation pathway of C-S-H during cement hydration from atomistic simulations
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
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Article
| Open AccessThe unusual quadruple bonding of nitrogen in ThN
Nitrogen can form a maximum of three shared electron-pair bonds to complete its octet, suggesting the maximum bond order of nitrogen is three. Here, the authors report a joint photoelectron spectroscopy and quantum chemical study, showing a quadruple bond between nitrogen and thorium in thorium nitride.
- Zejie Fei
- , Jia-Qi Wang
- & Jun Li
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Article
| Open AccessCation-induced changes in the inner- and outer-sphere mechanisms of electrocatalytic CO2 reduction
The underlying mechanism of cation effects on CO2RR remains debated. Combining constrained density function theory, Marcus theory, and slow-growth sampling approaches, we resolve how cations modulate the inner- and outer-sphere pathways of CO2RR at solid-liquid interfaces.
- Xueping Qin
- , Heine A. Hansen
- & Marko M. Melander
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Article
| Open AccessGenome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints
Analysis of CRISPR-Cas off-targets is important. Here the authors incorporate molecular dynamics simulations in the computational analysis of CRISPR editing and report the CRISOT tool suite and apply this to genome-wide CRISPR off-target prediction and sgRNA optimisation.
- Qinchang Chen
- , Guohui Chuai
- & Qi Liu
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Article
| Open AccessData-driven discovery of electrocatalysts for CO2 reduction using active motifs-based machine learning
Conventional ab initio calculations and machine learning provide limited information on catalytic activity and selectivity and often show discrepancy with experimental results. Here, the authors report a high-throughput virtual screening strategy to identify active and selective catalysts, leading to the discovery of Cu-Ga and Cu-Pd catalysts for CO2 electroreduction.
- Dong Hyeon Mok
- , Hong Li
- & Seoin Back
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Article
| Open AccessAn invertible, invariant crystal representation for inverse design of solid-state materials using generative deep learning
The lack of invertible and invariant crystal representations hinders the inverse design of crystals. Here the authors develop SLICES, an invertible and invariant representation, empowering property-driven inverse design of crystals using generative AI.
- Hang Xiao
- , Rong Li
- & Lei Wang
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Article
| Open AccessThermal dependence of the hydrated proton and optimal proton transfer in the protonated water hexamer
Water’s pivotal role is tied to the quantum nature of its hydrogen bond dynamics. Here, the authors investigate the thermal behavior of the protonated water hexamer through accurate path integral molecular dynamics, revealing that near-room temperature conditions are optimal for proton transfer.
- Félix Mouhat
- , Matteo Peria
- & Michele Casula
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Article
| Open AccessKnowledge-driven design of solid-electrolyte interphases on lithium metal via multiscale modelling
The application of Li metal electrodes in rechargeable batteries is limited by inherent high reactivity. Here, the authors provide model-based insights into the composition and formation mechanisms of the solid-electrolyte interphase on the µs-scale and suggest design strategies for the interphase.
- Janika Wagner-Henke
- , Dacheng Kuai
- & Ulrike Krewer
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Article
| Open AccessHighly active, ultra-low loading single-atom iron catalysts for catalytic transfer hydrogenation
Highly effective and selective noble metal-free catalysts continue to attract significant attention but require reaction specific tuning. Here, the authors fabricate a single-atom iron catalyst at low loading, which shows excellent transfer hydrogenation performance even at low reaction temperatures.
- Zhidong An
- , Piaoping Yang
- & Dionisios G. Vlachos
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Article
| Open AccessMulti-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling
Placing an organic material in an optical cavity can enhance exciton transport, but the mechanism is poorly understood. Here, using molecular dynamics simulations, the authors obtained atomistic insights into that mechanism.
- Ilia Sokolovskii
- , Ruth H. Tichauer
- & Gerrit Groenhof
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Article
| Open AccessStructural basis of dimerization of chemokine receptors CCR5 and CXCR4
Here, authors report chemokine receptors structures obtained using coarse-grained metadynamics. CCR5 and CXCR4 homo- and heterodimers differ in the conformations of ligand binding sites and of the G protein interaction interface, suggesting structural basis for the rational design of biased ligands.
- Daniele Di Marino
- , Paolo Conflitti
- & Vittorio Limongelli
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Article
| Open AccessChallenging an old paradigm by demonstrating transition metal-like chemistry at a neutral nonmetal center
The scope of and knowledge about the chemistry of nonmetal-adducts remains very limited. Here, the authors describe nonmetal adducts of the phosphorus center of terminal phosphinidene complexes using classical C- and N-ligands from metal coordination chemistry.
- David Biskup
- , Gregor Schnakenburg
- & Rainer K. Streubel
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Article
| Open AccessUniversal machine learning for the response of atomistic systems to external fields
External fields, despite their significant influence on chemical processes, have been largely ignored in current machine learning potentials. Here, the authors introduce a field-induced model that captures system-field interactions rigorously.
- Yaolong Zhang
- & Bin Jiang
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Article
| Open AccessMachine learning electronic structure methods based on the one-electron reduced density matrix
Electronic structure methods are vital, yet they are often too computationally expensive. Here, the authors develop machine learned density matrices to fully represent electronic structures in a computationally cheap and accurate way.
- Xuecheng Shao
- , Lukas Paetow
- & Michele Pavanello
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Article
| Open AccessControlling piezoresistance in single molecules through the isomerisation of bullvalenes
The quest for miniaturisation of electromechanical nanosystems requires the use of single molecules as active components. Here, the authors develop a piezoresistor based on a single bullvalene molecule that changes its shape by a Cope rearrangement.
- Jeffrey R. Reimers
- , Tiexin Li
- & Nadim Darwish
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Article
| Open AccessMachine learning coarse-grained potentials of protein thermodynamics
Understanding protein dynamics is a complex scientific challenge. Here, authors construct coarse-grained molecular potentials using artificial neural networks, significantly accelerating protein dynamics simulations while preserving their thermodynamics.
- Maciej Majewski
- , Adrià Pérez
- & Gianni De Fabritiis
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Article
| Open AccessResonating holes vs molecular spin-orbit coupled states in group-5 lacunar spinels
Dressing is a concept used to describe moderately interacting electrons. Here authors present the notion of dressed spin-orbit 3/2 moments and how this picture breaks down with increasing electronic interactions across group-5 lacunar spinel magnets.
- Thorben Petersen
- , Pritam Bhattacharyya
- & Liviu Hozoi
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Article
| Open AccessMinimizing non-radiative decay in molecular aggregates through control of excitonic coupling
Exciton delocalization in molecular aggregates is suggested to counteract the Energy Gap Law. Here, authors reveal the underlying physical picture and find the optimal excitonic coupling that minimizes nonradiative decay by nearly exact simulations.
- Yuanheng Wang
- , Jiajun Ren
- & Zhigang Shuai
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Article
| Open AccessTheory predicts UV/vis-to-IR photonic down conversion mediated by excited state vibrational polaritons
Vibrational polaritons steer chemical reactions and control quantum states for information processing. Here the authors predict their formation during electronic photo-excitation, enabling a down-conversion of visible to infrared photons.
- Connor K. Terry Weatherly
- , Justin Provazza
- & Roel Tempelaar
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Article
| Open AccessSynergy of dual-atom catalysts deviated from the scaling relationship for oxygen evolution reaction
The utilization of dual-atom catalysts holds the potential in surpassing single-atom catalysts for oxygen evolution reactions. Here, the authors examine the mechanism of dual-atom catalysts for oxygen evolution reaction and identify catalyst optimization recipes via large-scale computations.
- Cong Fang
- , Jian Zhou
- & Xiaoyan Sun
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Article
| Open AccessActinide inverse trans influence versus cooperative pushing from below and multi-center bonding
Actinide-ligand bonds with high multiplicities remain poorly understood. Here, the authors investigate covalency in actinide complexes and identify terminal O and N ligands that are triply to quadruply bonded to the actinide, facilitated by electrostatic, steric, and covalent interactions.
- Laura C. Motta
- & Jochen Autschbach
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Article
| Open AccessPotential-dependent transition of reaction mechanisms for oxygen evolution on layered double hydroxides
The mechanisms for oxygen evolution reaction on layered double hydroxides remain controversial. Here, the authors use a computational methodology by combining grand-canonical methods and microkinetic modeling to unravel the potential-dependent transitions mechanisms for electrochemical reactions.
- Zeyu Wang
- , William A. Goddard III
- & Hai Xiao
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Article
| Open AccessTemperature-pressure phase diagram of confined monolayer water/ice at first-principles accuracy with a machine-learning force field
Understanding the phase behaviour of nanoconfined water is of importance in science & engineering. Here the authors use machine-learning force field molecular dynamics to report two new quasi-bilayer ice phases in the phase diagram of monolayer ices.
- Bo Lin
- , Jian Jiang
- & Lei Li
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Article
| Open AccessQuantum simulation of exact electron dynamics can be more efficient than classical mean-field methods
It is often assumed that systems that can be analyzed accurately via mean-field theory would not be worth looking at using quantum algorithms, given entanglement plays no key role. Here, the authors show instead that a quantum advantage can be expected for simulating the exact time evolution of such electronic systems.
- Ryan Babbush
- , William J. Huggins
- & Joonho Lee