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Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Understanding the strain energy density in materials under axial load is crucial for evaluating their mechanical behavior and durability. When a rod is subjected to such a load, it elongates and stores energy, known as strain energy, as potential energy within the material. This energy is measured in terms of energy per unit volume.
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Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
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Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that...
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Wiggle150: Benchmarking Density Functionals and Neural Network Potentials on Highly Strained Conformers.

Rebecca R Brew1, Ian A Nelson1, Meruyert Binayeva1

  • 1Michigan State University, Lansing 48824, Michigan, United States.

Journal of Chemical Theory and Computation
|April 11, 2025
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Summary
This summary is machine-generated.

A new benchmark, Wiggle150, addresses the need for evaluating computational methods on strained molecular geometries. It reveals robust performance in methods like AIMNet2 for nonequilibrium systems.

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Area of Science:

  • Computational Chemistry
  • Quantum Chemistry
  • Method Development

Background:

  • Existing computational benchmarks primarily focus on equilibrium geometries.
  • This limits the assessment of methods for nonequilibrium structures crucial in molecular dynamics and reaction path exploration.
  • There is a need for benchmarks representing highly strained molecular conformations.

Purpose of the Study:

  • Introduce Wiggle150, a novel benchmark set of 150 highly strained molecular conformations.
  • Evaluate the performance of diverse computational methods in predicting relative energies for these challenging geometries.
  • Identify methods suitable for applications involving nonequilibrium molecular structures.

Main Methods:

  • Generated 150 highly strained conformations for adenosine, benzylpenicillin, and efavirenz using metadynamics.
  • Calculated reference energies using high-level composite quantum chemical methods (DLPNO-CCSD(T)/CBS).
  • Assessed various computational approaches: density-functional theory (DFT), composite methods, semiempirical models, neural network potentials (NNPs), and force fields.

Main Results:

  • Wiggle150 geometries exhibit significantly larger deviations in structural parameters and relative energies compared to existing benchmarks.
  • Multiple computational methods demonstrate a favorable speed-accuracy trade-off on the Wiggle150 set.
  • AIMNet2 emerged as a particularly robust neural network potential for predicting relative energies of strained conformations.

Conclusions:

  • Wiggle150 serves as a valuable tool for validating computational protocols for nonequilibrium systems.
  • The benchmark can guide the development of improved density functionals and neural network potentials.
  • This work advances the accuracy and robustness assessment of computational chemistry methods.