Constrained Broyden Minimization Combined with the Dimer Method for Locating Transition State of Complex Reactions

Shang, Cheng; Liu, Zhi-Pan

doi:10.1021/ct9005147

Cited by 97 publications

(99 citation statements)

References 52 publications

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“…Finally, we utilize the DESW method 34 to identify the TSs explicitly for all the IS/FS pairs 36 . The TS is confirmed by extrapolating the TS towards the IS and FS and the numerical vibrational frequency analysis.…”

Section: Reaction Pathway Sampling Based On Ssw Methodsmentioning

confidence: 99%

Nature of Rutile Nuclei in Anatase-to-Rutile Phase Transition

2015

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The solid phase transition of TiO2, in particular anatase to rutile, has been extensively studied in the past 30 years. To seek the nucleation site at the beginning of phase transition is highly challenging, which asks for new theoretical techniques with high spatial and temporal resolution. This work reports the first evidence on the atomic structure of the nucleation sites in the TiO2 anatase-to-rutile phase transition. Novel automated theoretical methods, namely stochastic surface walking based pathway sampling methods, are utilized to resolve the lowest energy pathways at the initial stage of phase transition. We show that among common anatase surfaces, only the (112) ridged surface provides the nucleation site for phase transition, which can lead to the formation of both TiO2-II and brookite thin slabs. The TiO2-II phase is kinetically preferred product; the propagation into the subsurface is still hindered by high barriers that is the origin for the slow kinetics of nuclei formation. The rutile nuclei are thus not rutile phase but nascent metastable TiO2-II phase in an anatase matrix. The phase transition kinetics is found to be sensitive to the compressive strain and the crystallographic directions. The results rationalize the size and morphology dependence of the anisotropic phase transition kinetics of anatase particles and could facilitate the rational design of material via controlled solid phase transition.

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Section: Reaction Pathway Sampling Based On Ssw Methodsmentioning

confidence: 99%

Nature of Rutile Nuclei in Anatase-to-Rutile Phase Transition

2015

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“…Instead, the first-derivative-based methods are widely utilized for locating the TS of surface reactions, which are in general highly demanding in computational power. The typical methods utilized include nudged-elasticband (NEB) method [43], the bond constrained methods [44], dimer-based method [45,46], and synchronous transit methods [47]. Rcently, Liu and coworkers developed the Constrained-Broyden-Minimization method [44] and Constrained-Broyden-dimer methods [46], which are found to be efficient for finding the TS of complex reactions on surface.…”

Section: Theoretical Methods For Modeling Heterogeneous Reactionsmentioning

confidence: 99%

Mechanism and kinetics for methanol synthesis from CO2/H2 over Cu and Cu/oxide surfaces: Recent investigations by first-principles-based simulation

Sun

Liu

2011

Front. Chem. China

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The efficient fixation and utilization of CO 2 has been consistently pursued by chemists for decades. Although Cu-based catalysts, e.g., Cu/ZnO/Al 2 O 3 , have been widely used in industry for methanol synthesis from CO 2 hydrogenation (CO 2 + 3H 2 !H 3 COH + H 2 O), many issues on the mechanism and the kinetics remain largely uncertain. For example, the surface site for CO 2 activation and the synergetic effect between Cu and oxide have been hotly debated in literature. In the past few years, theoretical modeling on pure Cu surfaces and Cu/oxide interfaces has been utilized to provide insight into these important questions. Here we will review the recent theoretical advances on simulating this complex heterogeneous catalytic process with first principles density functional theory (DFT) calculations and kinetics modeling. The theoretical results on the mechanism and the kinetics are compared and summarized.

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“…The TS location is then performed from the highest energy image point (Emax) at the pseudo pathway using the single-ended CBD TS searching method 38 . The surface walking involves the repeated bias potential addition and local relaxation with biased-CBD method to correct the walking direction, in a manner similar to the SSW and BP-CBD method.…”

Section: Figurementioning

confidence: 99%

Reaction sampling and reactivity prediction using the stochastic surface walking method

Zhang

Liu

2015

Phys. Chem. Chem. Phys.

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The prediction of chemical reactivity and thus the design of new reaction systems are the key challenges in chemistry. Here, we develop an unbiased general-purpose reaction sampling method, the stochastic surface walking based reaction sampling (SSW-RS) method, and show that the new method is a promising solution for reactivity prediction of complex reaction systems. The SSW-RS method is capable of sampling both the configuration space of the reactant and the reaction space of pathways, owing to the combination of two recently developed theoretical methods, namely, the stochastic surface walking (SSW) method for potential energy surface (PES) exploration and the double-ended surface walking (DESW) method for building pathways. By integrating with first principles calculations, we show that the SSW-RS method can be applied to investigate the kinetics of complex organic reactions featuring many possible reaction channels and complex hydrogen-bonding networks, as demonstrated here using two examples, epoxypropane hydrolysis in aqueous solution and β-d-glucopyranose decomposition. Our results show that simultaneous sampling of the soft hydrogen-bonding conformations and the chemical reactions involving hard bond making/breaking can be achieved in the SSW-RS simulation, and the mechanism and kinetics can be predicted without a priori information on the system. Unexpected new chemistry for these reactions is revealed and discussed. In particular, despite many possible pathways for β-d-glucopyranose decomposition, the SSW-RS shows that only β-d-glucose and levoglucosan are kinetically preferred direct products and the 5- or 7-member ring products should be secondary products derived from β-d-glucose or levoglucosan. As a general tool for reactivity prediction, the SSW-RS opens a new route for the design of rational reactions.

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Constrained Broyden Minimization Combined with the Dimer Method for Locating Transition State of Complex Reactions

Cited by 97 publications

References 52 publications

Nature of Rutile Nuclei in Anatase-to-Rutile Phase Transition

Nature of Rutile Nuclei in Anatase-to-Rutile Phase Transition

Mechanism and kinetics for methanol synthesis from CO2/H2 over Cu and Cu/oxide surfaces: Recent investigations by first-principles-based simulation

Reaction sampling and reactivity prediction using the stochastic surface walking method

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