Computational chemistry articles within Nature

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• Article | 05 July 2023

  Optimality guarantees for crystal structure prediction

  An algorithm has been developed that can provably predict the lowest energy structure of crystalline materials using a combination of combinatorial optimization and integer programming.

  • Vladimir V. Gusev
  • , Duncan Adamson
  •  & Matthew J. Rosseinsky

• Article | 15 March 2023

  Structural basis of odorant recognition by a human odorant receptor

  Through the use of cryo-electron microscopy and molecular dynamics stimulations, mechanistic insight into the binding of an odorant to the human odorant receptor OR51E2 is provided.

  • Christian B. Billesbølle
  • , Claire A. de March
  •  & Aashish Manglik

• Article | 14 September 2022

  The first-principles phase diagram of monolayer nanoconfined water

  Monolayer water exhibits rich and diverse phase behaviour that is highly sensitive to temperature and the van der Waals pressure acting within the nanochannel.

  • Venkat Kapil
  • , Christoph Schran
  •  & Angelos Michaelides

• Review Article | 01 June 2022

  The road to fully programmable protein catalysis

  Recent progress in computational enzyme design, active site engineering and directed evolution are reviewed, highlighting methodological innovations needed to deliver improved designer biocatalysts.

  • Sarah L. Lovelock
  • , Rebecca Crawshaw
  •  & Anthony P. Green

• Matters Arising | 23 March 2022

  [{Th(C₈H₈)Cl₂}₃]²⁻ is stable but not aromatic

  • Ben Joseph R. Cuyacot
  •  & Cina Foroutan-Nejad

• Article | 10 February 2020

  Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

  A computational screen of an ultra-large virtual library against the structure of the melatonin receptor found nanomolar ligands, and ultimately two selective MT₁ inverse agonists that induced phase advancement of the mouse circadian clock when given at subjective dusk.

  • Reed M. Stein
  • , Hye Jin Kang
  •  & Margarita L. Dubocovich

• Letter | 18 September 2019

  Low-barrier hydrogen bonds in enzyme cooperativity

  Structural and biophysical studies reveal that low-barrier hydrogen bonds enable long-range communication between the active sites of multimeric enzymes and synchronise catalysis.

  • Shaobo Dai
  • , Lisa-Marie Funk
  •  & Kai Tittmann

• Article | 08 May 2019

  Time-resolved protein activation by proximal decaging in living systems

  The authors report a general strategy for in vivo protein activation using light-controlled proximal decaging directed by in silico screening.

  • Jie Wang
  • , Yuan Liu
  •  & Peng R. Chen

• Review Article | 25 July 2018

  Machine learning for molecular and materials science

  Recent progress in machine learning in the chemical sciences and future directions in this field are discussed.

  • Keith T. Butler
  • , Daniel W. Davies
  •  & Aron Walsh

• Letter | 14 May 2018

  The effect of hydration number on the interfacial transport of sodium ions

  A sodium ion hydrated with three (rather than one, two, four or five) water molecules diffuses orders of magnitude more quickly than the other ion hydrates owing to the interfacial symmetry mismatch.

  • Jinbo Peng
  • , Duanyun Cao
  •  & Ying Jiang

• Letter | 07 October 2015

  Peptoid nanosheets exhibit a new secondary-structure motif

  Some peptoids—synthetic structural relatives of polypeptides—can assemble into two-dimensional nanometre-scale sheets; simulations and experimental measurements show that these nanosheets contain a motif unique to peptoids, namely zigzag Σ-strands, which interlock and enable the nanosheets to extend in two dimensions only.

  • Ranjan V. Mannige
  • , Thomas K. Haxton
  •  & Stephen Whitelam

• Letter | 12 March 2014

  Interrogating selectivity in catalysis using molecular vibrations

  A set of parameters based on the response of a molecule’s properties to infrared vibrations can be used to model and predict selectivity trends for molecular reactions with interlinked steric and electronic effects at positions of interest

  • Anat Milo
  • , Elizabeth N. Bess
  •  & Matthew S. Sigman

• Letter | 10 July 2013

  Metal-free oxidation of aromatic carbon–hydrogen bonds through a reverse-rebound mechanism

  Phthaloyl peroxide functions as a selective oxidant of C–H bonds in the transformation of arenes to phenols under mild conditions, in a reaction that is compatible with a wide array of functional groups.

  • Changxia Yuan
  • , Yong Liang
  •  & Dionicio Siegel

• News & Views | 10 June 2012

  Computer model predicts side effects

  Drug candidates are usually found to be unsafe only late in the drug discovery process. A method for predicting the many biological targets of a given molecule might allow drug safety to be considered much earlier. See Article p.361

  • Kyle Kolaja

• News & Views | 05 January 2011

  DNA as a logic operator

  Computers use transistor-based logic gates as the basis of their functions, but molecular logic gates would make them much faster. A report of DNA-based logic gates could be a first step towards molecular computing.

  • Thomas Carell

• News & Views | 30 June 2010

  Pulled from a protein's embrace

  It is hard to predict how strongly a small molecule will bind to a protein, but this is a crucial goal of computer-aided drug discovery. A new approach models the forcible removal of molecules from a protein's active site.

  • William L. Jorgensen