Minima hopping guided path search: An efficient method for finding complex chemical reaction pathways

Principles of isomer stability in small clusters

In this work we study isomers of several representative small clusters to find principles for their stability. Our conclusions about the principles underlying the structure of clusters are based on a huge database of 44 000 isomers generated for 58 different clusters on the density functional theory level by Minima Hopping. We explore the potential energy surface of small neutral, anionic and cationic isomers, moving left to right across the third period of the periodic table and varying the number of atoms n and the cluster charge state q (X ^q _n , with X = {Na, Mg, Al, Si, Ge}, q = -1, 0, 1, 2). We use structural descriptors such as bond lengths and atomic coordination numbers, the surface to volume ratios and the shape factor as well as electronic descriptors such as shell filling and hardness to detect correlations with the stability of clusters. The isomers of metallic clusters are found to be structure seekers with a strong tendency to adopt compact shapes. However certain numbers of atoms can suppress the formation of nearly spherical metallic clusters. Small non-metallic clusters typically also do not adopt compact spherical shapes for their lowest energy structures. In both cases spherical jellium models are not any more applicable. Nevertheless for many structures, that frequently have a high degree of symmetry, the Kohn-Sham eigenvalues are bunched into shells and if the available electrons can completely fill such shells, a particularly stable structure can result. We call such a cluster whose shape gives rise to shells that can be completely filled by the number of available electrons an optimally matched cluster, since both the structure and the number of electrons must be special and match. In this way we can also explain the stability trends for covalent silicon and germanium cluster isomers, whose stability was previously explained by the presence of certain structural motifs. Thus we propose a unified framework to explain trends in the stability of isomers and to predict their structure for a wide range of small clusters.

New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited

The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH₃ (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.

AutoMeKin2021: An open-source program for automated reaction discovery

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

Finding Reaction Pathways with Optimal Atomic Index Mappings

Finding complex reaction and transformation pathways involving many intermediate states is, in general, not possible on the density-functional theory level with existing simulation methods, due to the very large number of required energy and force evaluations. For complex reactions, it is not possible to determine which atom in the reactant is mapped onto which atom in the product. Trying out all possible atomic index mappings is not feasible because of the factorial increase in the number of possible mappings. We use a penalty function that is invariant under index permutations to bias the potential energy surface in such a way that it obtains the characteristics of a structure seeker, whose global minimum is the reaction product. By performing a minima-hopping-based global optimization on this biased potential energy surface, we rapidly find intermediate states that lead into the global minimum and allow us to then extract entire reaction pathways. We first demonstrate for a benchmark system, namely, the Lennard-Jones cluster LJ_{38}, that our method finds intermediate states relevant to the lowest energy reaction pathway, and hence we need to consider much fewer intermediate states than previous methods to find the lowest energy reaction pathway. Finally, we apply the method to two real systems, C_{60} and C_{20}H_{20}, and show that the reaction pathways found contain valuable information on how these molecules can be synthesized.

Phase Transition Pathway Sampling via Swarm Intelligence and Graph Theory

The prediction of reaction pathways for solid-solid transformations remains a key challenge. Here, we develop a pathway sampling method via swarm intelligence and graph theory and demonstrate that our pallas method is an effective tool to help understand phase transformations in solid-state systems. The method is capable of finding low-energy transition pathways between two minima without having to specify any details of the transition mechanism a priori. We benchmarked our pallas method against known phase transitions in cadmium selenide (CdSe) and silicon (Si). pallas readily identifies previously reported, low-energy phase transition pathways for the wurtzite to rock-salt transition in CdSe and reveals a novel lower-energy pathway that has not yet been observed. In addition, pallas provides detailed information that explains the complex phase transition sequence observed during the decompression of Si from high pressure. Given the efficiency to identify low-barrier-energy reaction pathways, the pallas methodology represents a promising tool for materials by design with valuable insights for novel synthesis.

Understanding CO oxidation on the Pt(111) surface based on a reaction route network

Kinetic analysis by the rate constant matrix contraction on the reaction route network of CO oxidation on the Pt(111) surface obtained by the artificial force induced reaction reveals the impact of entropic contributions arising from a variety of local minima and transition states.

TGMin: An efficient global minimum searching program for free and surface-supported clusters

In this article, we introduce an efficient global-minimum structural search program named Tsinghua Global Minimum 2 (TGMin-2), which is the successor of the original TGMin algorithm that was developed in our group in 2011. We have introduced a number of new features and improvements into TGMin-2, including a symmetric structure generation algorithm that can produce good initial seeds for small- and medium-size clusters, the duplicated structure identification algorithm, and the improved structure adaption algorithm that was implemented in the original TGMin code. To predict the simulated photoelectron spectrum (PE spectrum) automatically, we also implemented a standalone program named AutoPES (Auto Photoelectron Spectroscopy), which can be used to simulate PE spectra and compare them with experimental results automatically. We have demonstrated that TGMin-2 and AutoPES are powerful tools for studying free and surface-supported molecules, clusters, and nanoclusters. © 2018 Wiley Periodicals, Inc.

A Trajectory-Based Method to Explore Reaction Mechanisms

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Towards operando computational modeling in heterogeneous catalysis

An increased synergy between experimental and theoretical investigations in heterogeneous catalysis has become apparent during the last decade. Experimental work has extended from ultra-high vacuum and low temperature towards operando conditions. These developments have motivated the computational community to move from standard descriptive computational models, based on inspection of the potential energy surface at 0 K and low reactant concentrations (0 K/UHV model), to more realistic conditions. The transition from 0 K/UHV to operando models has been backed by significant developments in computer hardware and software over the past few decades. New methodological developments, designed to overcome part of the gap between 0 K/UHV and operando conditions, include (i) global optimization techniques, (ii) ab initio constrained thermodynamics, (iii) biased molecular dynamics, (iv) microkinetic models of reaction networks and (v) machine learning approaches. The importance of the transition is highlighted by discussing how the molecular level picture of catalytic sites and the associated reaction mechanisms changes when the chemical environment, pressure and temperature effects are correctly accounted for in molecular simulations. It is the purpose of this review to discuss each method on an equal footing, and to draw connections between methods, particularly where they may be applied in combination.

Implementation and performance of the artificial force induced reaction method in the GRRM17 program

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways

We describe a flexible and broadly applicable energy refinement method, "nebterpolation," for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation. The new method is applicable to ab initio simulations with hundreds of atoms containing complex and multimolecular reaction events. A key aspect of nebterpolation is smoothing of the reactive MD trajectory in internal coordinates to initiate the search for the reaction path on the potential energy surface. We apply nebterpolation to analyze the reaction events in an ab initio nanoreactor simulation that discovers new molecules and mechanisms, including a C-C coupling pathway for glycolaldehyde synthesis. We find that the new method, which incorporates information from the MD trajectory that connects reactants with products, produces a dramatically distinct set of minimum energy paths compared to existing approaches that start from information for the reaction end points alone. The energy refinement method described here represents a key component of an emerging simulation paradigm where molecular dynamics simulations are applied to discover the possible reaction mechanisms.

Reaction sampling and reactivity prediction using the stochastic surface walking method

The new theoretical method demonstrates the ability of automated reaction sampling and activity prediction for complex organic reactions.

Multipole-preserving quadratures for the discretization of functions in real-space electronic structure calculations

Discretizing an analytic function on a uniform real-space grid is often done via a straightforward collocation method.

Isomerism and structural fluxionality in the Au26 and Au26(-) nanoclusters

Using the minima hopping global optimization method at the density functional level, we found low-energy nanostructures for neutral Au26 and its anion. The local-density and a generalized gradient approximation of the exchange–correlation functional predict different nanoscale motifs. We found a vast number of isomers within a small energy range above the respective putative global minima with each method. Photoelectron spectroscopy of Au26(-) under different experimental conditions revealed definitive evidence of the presence of multiple isomers, consistent with the theoretical predictions. Comparison between the experimental and simulated photoelectron spectra suggests that the photoelectron spectra of Au26(-) contain a mixture of three isomers, all of which are low-symmetry core–shell-type nanoclusters with a single internal Au atom. We present a disconnectivity graph for Au26(-) that has been computed completely at the density functional level. The transition states used to build this disconnectivity graph are complete enough to predict Au26(-) to have a possible fluxional shell, which facilitates the understanding of its catalytic activity.