Molecular dynamics articles within Nature Chemistry

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  • Article
    | Open Access

    Atomistic simulations have a broad range of applications from drug design to materials discovery. Machine learning interatomic potentials (MLIPs) have become an efficient alternative to computationally expensive ab initio simulations. Now a general reactive MLIP (called ANI-1xnr) has been developed and validated against a broad range of condensed-phase reactive systems.

    • Shuhao Zhang
    • , Małgorzata Z. Makoś
    •  & Justin S. Smith

  • Article
    | Open Access

    The organization of electrolytes at the air/water interface affects the structure of interfacial water and therefore numerous natural processes. It has now been demonstrated that the surface of an electrolyte solution is stratified and consists of an ion-depleted outer surface and an ion-enriched subsurface layer, jointly determining the water interfacial structure.

    • Yair Litman
    • , Kuo-Yang Chiang
    •  & Mischa Bonn

  • Article
    | Open Access

    Electronic spin influences chemistry profoundly, but its role in surface chemistry is poorly established. Now the spin-dependent reaction probabilities of oxygen atoms with a graphite surface have been studied. Molecular dynamics simulations help elucidate the mechanism for spin-flipping, which is observed to occur with low probability in surface scattering experiments.

    • Zibo Zhao
    • , Yingqi Wang
    •  & G. Barratt Park

  • Article |

    Molecular energy transfer is thought to follow a simple rule of thumb: high energy transfer requires hard collisions that result in backscattering. However, now it has been observed that an unexpected forward scattering occurs in NO–CO and NO–HD collisions even for high energy transfer. This is attributed to ‘hard-collision glory scattering’, a mechanism that appears to be ubiquitous in molecule–molecule collisions.

    • Matthieu Besemer
    • , Guoqiang Tang
    •  & Tijs Karman

  • Article |

    As the number of atoms involved in a reaction increases, so do the experimental and theoretical challenges faced when studying their dynamics. Now, using ion-imaging experiments and quasi-classical trajectory simulations, the dynamics of the polyatomic reaction F– + CH3CH2Cl have been studied and the competition between bimolecular nucleophilic substitution and base-induced elimination has been disentangled.

    • Jennifer Meyer
    • , Viktor Tajti
    •  & Roland Wester

  • Article |

    Simulations of the SARS-CoV-2 proteome that include over 0.1 s of aggregate data are reported. Spike opening was observed, revealing cryptic epitopes that differ between variants, explaining differential interactions with antibodies and receptors that determine pathogenicity. The cryptic pockets described provide new targets for antivirals and a wealth of mechanistic insight.

    • Maxwell I. Zimmerman
    • , Justin R. Porter
    •  & Gregory R. Bowman

  • Article |

    Recent experiments reporting the isomerization of CO on a NaCl(100) surface—from C adsorbed to O adsorbed—represent a major challenge to simulate from first principles. Now, using dynamics calculations and (CO–NaCl)n cluster models that feature CO–CO interactions, it is found that isomerization occurs via a ‘roaming’ mechanism at a large distance from the NaCl(100) surface.

    • Apurba Nandi
    • , Peng Zhang
    •  & Joel M. Bowman

  • Article |

    The structure and dynamics of hydrogen bonds in ion hydration shells are not yet fully understood, however, small ion–dihydrate molecular complexes represent ideal model systems with which to investigate the interplay between ion–water and water–water interactions. Now, state-of-the-art quantum dynamics simulations have provided evidence for tunnelling in hydrogen-bond rearrangements in the iodide–dihydrate complex.

    • Pushp Bajaj
    • , Jeremy O. Richardson
    •  & Francesco Paesani

  • News & Views |

    State-of-the-art quantum simulations predict that solvent molecules may partner with a solute in solution to form stable chemically distinct coordination species that interconvert from one to another. The solvent would thus be directly implicated in chemical reactions.

    • Gilles H. Peslherbe

  • News & Views |

    Potassium channels rapidly move K+ ions across cell membranes while blocking Na+, but how these two effects are achieved simultaneously has remained unclear. Now, extensive molecular simulations show a single mechanism that features fully dehydrated ions can explain both rapid transport and impeccable selectivity.

    • Ben Corry

  • Article |

    That K+ channels conduct K+ ions at near-diffusion limited rates, but block the passage of smaller Na+ ions, creates an apparent contradiction. Now, atomistic simulations and free-energy calculations are used to show that both K+ permeation and ion selectivity are governed by the direct knock-on of completely desolvated ions in the channels’ selectivity filter.

    • Wojciech Kopec
    • , David A. Köpfer
    •  & Ulrich Zachariae

  • Article |

    Molecular dynamics simulations for seven members of the Src kinase family have now revealed a conserved step-wise deactivation process, potentially druggable intermediate states, and quantitatively similar thermodynamics and kinetics across the entire family.

    • Mohammad M. Sultan
    • , Gert Kiss
    •  & Vijay S. Pande

  • Article |

    Mixed quantum–classical molecular dynamics simulations of Na2 in liquid tetrahydrofuran have revealed that when local specific interactions between a solute and solvent are energetically on the same order as a hydrogen bond, the solvent controls not only bond dynamics but also the chemical identity of simple solutes.

    • Devon. R. Widmer
    •  & Benjamin J. Schwartz

  • Article |

    Collision-induced spin–orbit transitions involve multiple interaction potentials and are by nature non-adiabatic, complicating both their experimental and theoretical study. Crossed-beam experiments and non-Born–Oppenheimer quantum calculations for inelastic collisions of carbon atoms with helium atoms, down to energies corresponding to temperatures below 10 K, have now been performed. Quantum-dynamical resonances predicted by theory were experimentally detected.

    • Astrid Bergeat
    • , Simon Chefdeville
    •  & François Lique

  • Article |

    Calculations at the theoretical gold standard generally yield accurate results for a variety of energy-transfer processes in molecular collisions. Using anti-seeding methods in a crossed-beam inelastic scattering experiment, a resonance structure is clearly resolved for NO–H2 collisions, pushing the required accuracy for theoretical potentials beyond the gold standard.

    • Sjoerd N. Vogels
    • , Tijs Karman
    •  & Sebastiaan Y. T. van de Meerakker

  • Article |

    Uncovering the microscopic details of protein–protein association via direct molecular dynamics (MD) simulations has been prevented by the excessive lifetimes of associated states. Now, association and dissociation for the barnase–barstar complex has been studied by adaptive high-throughput MD simulations and Markov modelling, revealing intermediate structures, energetics and kinetics on microseconds-to-hours timescales.

    • Nuria Plattner
    • , Stefan Doerr
    •  & Frank Noé

  • Article |

    The controlled mechanical activation of specific covalent bonds is a rapidly expanding field in chemistry. Now, it is shown that disulfide bond reduction proceeds through different mechanisms depending on the external force applied. This strongly suggests that refined models should be used when interpreting mechanochemical experiments, particularly when sonication is involved.

    • Przemyslaw Dopieralski
    • , Jordi Ribas–Arino
    •  & Dominik Marx

  • Article |

    FeFe hydrogenases are highly efficient H2 producing enzymes; however, they can be inactivated by O2. Now, a mechanism for O2 diffusion within FeFe hydrogenases and its reactions at the active site of the enzyme has been proposed. These findings could help with the design of hydrogenase mutants with increased resistance to oxidative damage.

    • Adam Kubas
    • , Christophe Orain
    •  & Christophe Léger

  • News & Views |

    Understanding the minute details of CO2 transport is key to finding new technologies that reduce the hazardous levels of CO2 in our atmosphere. Now, the observation that the transport of CO2 in molten calcium carbonate occurs faster than standard molecular diffusion brings us one step closer.

    • Barbara Kirchner
    •  & Barbara Intemann

  • Article |

    An important source of atmospheric hydroxyl radicals is from the dissociation of Criegee intermediates produced in alkene ozonolysis reactions. The dissociation dynamics of the prototypical CH3CHOO Criegee intermediate have now been determined. Complementary experimental and theoretical studies were carried out and the translational and internal energy distributions of the OH radical products were characterized.

    • Nathanael M. Kidwell
    • , Hongwei Li
    •  & Marsha I. Lester

  • Article |

    A collaborative approach between experiment and simulation has revealed a single mutation in the F/G loop of the newly described nitrating cytochrome P450 TxtE that controls loop dynamics and, more surprisingly, the regioselectivity of the reaction. This mutation is present in a subset of homologous nitrating P450s that produce a previously unidentified biosynthetic intermediate, 5-nitro-L-tryptophan.

    • Sheel C. Dodani
    • , Gert Kiss
    •  & Frances H. Arnold

  • Article |

    The solvation behaviour of CO2 in carbonate melts is important from both a geochemical point of view and with respect to its electroreduction. Now, simulations have shown that solvation of CO2 in molten CaCO3 leads to the formation of the pyrocarbonate anion, C2O52–, which significantly enhances the transport of CO2 via a Grotthuss-like mechanism.

    • Dario Corradini
    • , François-Xavier Coudert
    •  & Rodolphe Vuilleumier

  • Article |

    The question of how divalent metal ions direct the folding of ribozymes is a major unsolved problem. A computational model has now been used to reveal the molecular mechanism by which Mg2+ drives the Azoarcus ribozyme into a catalytically functional state. Simulations also show that although Ca2+ drives folding it leaves the active site unstable.

    • Natalia A. Denesyuk
    •  & D. Thirumalai

  • News & Views |

    Molecular simulations have the potential to give valuable insights into experimental results, but can be limited by the time- and length-scales they can simulate. Now, reactive chemistry can be driven through a novel simulation approach, which could have ramifications for many research areas, including astrobiology and the origins of life.

    • Nir Goldman

  • Article |

    It is generally believed that, after being generated, an excess electron in water shrinks from a strongly delocalized to a localized state in about a picosecond. Now, these early stages in the behaviour of this electron have been observed using a combination of transient THz spectroscopy and ab initio molecular dynamics simulations.

    • Janne Savolainen
    • , Frank Uhlig
    •  & Pavel Jungwirth

  • Article |

    The adoption of multiple conformations by proteins presents a challenge for ligand discovery using docking simulations. Now, a method for representing the conformational behaviour of a flexible protein in docking screens, which is guided by experimental crystallography data, is shown to predict protein conformation, ligand pose and aid the discovery of new ligands.

    • Marcus Fischer
    • , Ryan G. Coleman
    •  & Brian K. Shoichet

  • News & Views |

    High selectivity is essential in the enzymatic biosynthesis of complex natural products. Now, the discovery of multiple sequential bifurcations on the reaction path towards the formation of a diterpenoid shows how dynamics affect selectivity, and suggests how enzymes may steer reactions towards a specific product.

    • Charles E. Hornsby
    •  & Robert S. Paton

  • Article |

    A terpene-forming carbocation reaction is described for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. Dynamic effects are shown to contribute to the selectivity of the reaction, with consequences for how enzymes control the biosynthesis of complex natural products.

    • Young Joo Hong
    •  & Dean J. Tantillo

  • News & Views |

    Lengthy molecular dynamics simulations of complex systems at the atomic scale usually require supercomputers. Now, by stitching together many shorter independent simulations run 'in the cloud', this requirement has been circumvented, allowing two milliseconds of the dynamics of a G-protein-coupled receptor to be simulated.

    • Xavier Deupi

  • Article |

    Two milliseconds of molecular dynamics simulations of a major drug-target G-protein-coupled receptor (GPCR) has been carried out using Google's Exacycle cloud computing platform. Markov state models were used to aggregate independent simulations into a statistical model that provides an atomistic description of GPCR ligand-modulated activation pathways.

    • Kai J. Kohlhoff
    • , Diwakar Shukla
    •  & Vijay S. Pande

  • Article |

    Using ab initio simulations external mechanical forces are shown to trigger structural changes to disulfide bridges that result in conformations that are less susceptible to nucleophilic attack. This finding is crucial for the interpretation of recent force microscopy experiments, and could be important for understanding protein regulation.

    • Przemyslaw Dopieralski
    • , Jordi Ribas-Arino
    •  & Dominik Marx

  • News & Views |

    Proton conduction in both water and other hydrogen-bonded liquids occurs through successive proton transfers along the hydrogen-bond network. But first-principles simulations have revealed that the mechanism by which this occurs in orthophosphoric acid has some unusual features.

    • Rodolphe Vuilleumier
    •  & Daniel Borgis

  • Article |

    Proton transport in phosphate-based systems is important in biology and clean energy technologies, and phosphoric acid, being the best known intrinsic proton conductor, represents an important model. Ab initio molecular dynamics simulations now reveal that the interplay between extended, polarized, hydrogen-bonded chains and a frustrated hydrogen-bond network gives rise to the high conductivity in liquid phosphoric acid.

    • Linas Vilčiauskas
    • , Mark E. Tuckerman
    •  & Klaus-Dieter Kreuer

  • Article |

    The flow of vibrational energy into reactants and out of products plays a critical role in nearly every chemical reaction. Here, a time-resolved ultrafast microscopic map of energy flow is provided for a thermal bimolecular chemical reaction that takes place in dichloromethane, a typical organic solvent.

    • David R. Glowacki
    • , Rebecca A. Rose
    •  & Jeremy N. Harvey

  • News & Views |

    Dynamic communication between atoms within folded proteins is potentially important for function, but its measurement has been a challenge. Now, a combined NMR and modelling study provides insights on the presence and strengths of such correlations.

    • Rafael Brüschweiler

  • Article |

    Selective reaction of one C–H bond among many in complex organic molecules is a grand challenge for organic chemistry. Here, starting from an enzyme that oxidizes two positions in a steroid without bias, laboratory evolution is used to prepare mutants that can regio- and stereoselectively oxidize either position.

    • Sabrina Kille
    • , Felipe E. Zilly
    •  & Manfred T. Reetz

  • Article |

    The formation of simple prebiotic organic compounds on early Earth is thought to be an important step in the origin of life. Molecular dynamics simulations of the conditions within cometary ice during planetary impact suggest a possible mechanism for the formation of glycine, an amino acid.

    • Nir Goldman
    • , Evan J. Reed
    •  & Amitesh Maiti

  • Research Highlights |

    Molecular dynamics simulations suggest that proton transfer in water within a carbon nanotube occurs through a mechanism different from that found in bulk water.

    • Gavin Armstrong

  • Article |

    Thermal reduction of graphene oxide is an attractive route towards the preparation of graphene, but complete removal of residual oxygen is problematic. Now, molecular dynamics simulations elucidate the chemical changes involved in this process.

    • Akbar Bagri
    • , Cecilia Mattevi
    •  & Vivek B. Shenoy

  • Research Highlights |

    Molecular dynamics simulations have revealed important mechanistic details about how carbamate is transported from one active site to another within in an enzyme.

    • Gavin Armstrong

  • Research Highlights |

    The motion of a molecule on a hot surface is investigated using molecular dynamics, revealing a regime of fast rolling and vibrational excitation.

    • Gavin Armstrong

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