Reaction Modeling Enhances Experiment

Computational Chemistry: Ab initio nanoreactor finds previously undetected products and mechanisms

Stu Borman

REACTIVE MOVIES

The Stanford group demonstrated the capabilities of their new ab initio nanoreactor by simulating reactions with different levels of molecular complexity: Acetylene polymerization (top) and the classic 1953 Urey-Miller reaction. The simulations generate products found experimentally in those reactions as well as others that have not. The acetylene simulation yielded nearly 100 distinct products, including methane, ethylene, cyclopropene, benzene, and larger polymeric species with aliphatic or aromatic character. The Urey-Miller simulation generated over 600 products, including urea, ethylene glycol, isocyanic acid, glycine, an alanine analog, and the unnatural amino acids α-hydroxyglycine and α-aminoglycine

Dark gray = carbon, red = oxygen, blue = nitrogen, white = hydrogen. Other colors (see filmstrip below) highlight newly formed molecules.

Credit: Courtesy of Lee-Ping Wang & Todd Martínez

A computational chemistry system developed this year further advanced a long-standing goal of theoretical chemistry—using theory to discover new reaction pathways and chemical products. The new system, called an “ab initio nanoreactor,” was devised by Todd J. Martínez and coworkers at Stanford University (Nat. Chem. 2014, DOI: 10.1038/nchem.2099). The approach uses ab initio molecular dynamics accelerated by graphical processing units (computer video cards) to simulate chemical reactions. In the simulations, the nanoreactor identifies some products already found by experimental means but also some not yet discovered—typically because chemists haven’t been able to re-create in the lab the high temperatures and pressures needed to make them. Martínez and coworkers used the system to simulate the polymerization of acetylene and the production of biomolecules and other complex products from simple compounds typical of those found on early Earth, similar to the classic 1953 Urey-Miller experiment. The computational system mixes and compresses compounds virtually and uses quantum mechanics to simulate bond breaking, bond formation, and molecular rearrangements. It tracks minimum-energy pathways between reactants and products to determine mechanisms. Computational chemistry expert Bernd Ensing of the University of Amsterdam commented that the nanoreactor needs refinement but that its development nevertheless “is an important pioneering milestone that may lead to a paradigm shift and a new way of thinking about performing in silico experiments. … As such simulations get more accurate and realistic, they will become more and more important to supplement and eventually replace parts of experimental chemistry.”

 Three frames from a 400-picosecond simulation of the classic Urey-Miller experiment. The reaction starts with simple compounds (left) and develops more complex ones as it proceeds (center and right). C = dark gray, O = red, N= blue, H = white. Other colors highlight newly formed molecules. Credit: Lee-Ping Wang & Todd Martínez

Three frames from a 400-picosecond simulation of the classic Urey-Miller experiment. The reaction starts with simple compounds (left) and develops more complex ones as it proceeds (center and right). C = dark gray, O = red, N= blue, H = white. Other colors highlight newly formed molecules.
Credit: Lee-Ping Wang & Todd Martínez

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