Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

A Multiscale Approach to Determination of Thermal Properties and Changes in Free Energy: Application to Reconstruction of Dislocations in Silicon

We introduce an approach to exploit the existence of multiple levels of description of a physical system to radically accelerate the determination of thermodynamic quantities. We first give a proof of principle of the method using two empirical interatomic potential functions. We then apply the technique to feed information from an interatomic potential into otherwise inaccessible quantum mechanical tight-binding calculations of the reconstruction of partial dislocations in silicon at finite temperature. With this approach, comprehensive ab initio studies at finite temperature will now be possible.Comment: 5 pages, 3 figure

Ab-initio Dynamics of Rare Thermally Activated Reactions

We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear degrees of freedom are coupled to a thermal bath, through a Langevin equation. This method is based on the path integral representation for the stochastic dynamics and yields the time evolution of both nuclear and electronic degrees of freedom, along the most probable reaction pathways, without spending computational time to explore metastable states. This approach is very efficient and allows to study thermally activated reactions which cannot be simulated using ab-initio molecular dynamics techniques. As a first illustrative application, we characterize the dominant pathway in the cyclobutene to butadiene reaction.Comment: 4 pages, 4 figure

Tight-binding molecular-dynamics studies of defects and disorder in covalently-bonded materials

Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between empirical methods which, while fast and efficient, lack transferability, and ab initio approaches which, because of excessive computational workload, suffer from limitations in size and run times. In this short review article, we examine several recent applications of TBMD in the area of defects in covalently-bonded semiconductors and the amorphous phases of these materials.Comment: Invited review article for Comput. Mater. Sci. (38 pages incl. 18 fig.

Molecular modeling for physical property prediction

Multiscale modeling is becoming the standard approach for process study in a broader framework that promotes computer aided integrated product and process design. In addition to usual purity requirements, end products must meet new constraints in terms of environmental impact, safety of goods and people, specific properties. This chapter adresses the use of molecular modeling tools for the prediction of physical property usefull for chemical engineering practice