Sebastian Brickel's research while affiliated with University of Basel and other places

Publications (12)

Preprint
Full-text available
The Menshutkin reaction is a methyl transfer reaction relevant in fields ranging from biochemistry to chemical synthesis. In the present work, energetics and solvent distributions for NH$_{3}$+MeCl and Pyr+MeBr reactions were investigated in the gas-phase, in water, methanol, acetonitrile, benzene, and in cyclohexane by means of reactive molecular...
Article
The kinetics of MgO⁺ + CH4 was studied experimentally using the variable ion source, temperature adjustable selected ion flow tube (VISTA-SIFT) apparatus from 300 - 600 K and computationally by running and analyzing reactive atomistic simulations. Rate coefficients and product branching fractions were determined as a function of temperature. The re...
Preprint
Full-text available
The kinetics of MgO$^+$ + CH$_4$ was studied experimentally using the variable ion source, temperature adjustable selected ion flow tube (VISTA-SIFT) apparatus from 300 $-$ 600 K and computationally by running and analyzing reactive atomistic simulations. Rates and product branching fractions were determined as a function of temperature. The reacti...
Article
The nucleophilic substitution reaction [Cl-CH3-Br]- is used for a comparative study of several reactive molecular dynamics schemes in the gas phase and in solution. Multi surface adiabatic reactive MD (MS-ARMD) and multi-state valence bond (MS-VALBOND) use empirical force fields to allow bond-breaking and bond-formation in dynamics studies. As a th...
Article
Understanding mechanistic aspects of reactivity lies at the heart of chemistry. Once the potential energy surface (PES) for a system of interest is known, reactions can be studied by computational means. While the minimum energy path (MEP) between two minima of the PES can give some insight into the topological changes required for a reaction to oc...
Article
The Claisen rearrangement is a carbon-carbon bond-forming, pericyclic reaction of fundamental importance due to its relevance in synthetic and mechanistic investigations of organic and biological chemistry. Despite continued efforts, the molecular origins of the rate acceleration in going from the aqueous phase into the protein is still incompletel...
Article
Full-text available
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further devel...
Article
Full-text available
Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by the time-independent Schrödinger equation within the Born-Oppenheimer approximation and to find...
Article
The OH-stretch induced dynamics in fluorosulfonic acid (HSO$_3$F) is characterized from a statistically significant number of trajectories using Multi-Surface Adiabatic Reactive Molecular Dynamics (MS-ARMD) simulations. The global reactive potential energy surface, which describes H-transfer and HF-elimination, is parametrized at the MP2/6-311G++(2...
Article
Vibrationally induced photodissociation in sulfurochloridic acid (HSO$_3$Cl) is found to be a viable process to form SO$_3$ and HCl from excitations of the OH-stretching overtone starting at $\nu_{\text{OH}} = 4$. Reactive molecular dynamics simulations on a fully-dimensional potential energy surface fitted to MP2 calculations show that hydrogen tr...

Citations

... Such a quality is comparable with that found in previous studies. The reactive PES for the hydrogen abstraction reaction between MgO + and ethane had a RMSD of 1.5 kcal/mol with respect to MP2/aug-cc-pVTZ for the reactant and 1.1 kcal/mol for the product state.81 For the Diels-Alder reaction between 2,3-dibromobutadiene and maleic anhydride had a RMSD of 2.9 kcal/mol for the overall reaction.82 ...
... Machine learning potential is one of the most critical calculations advances in recent years and has been intensively studied and applied in catalysis [112][113][114][115][116][117][118][119][120][121][122][123][124][125][126][127]. The machine learning potential is a method that uses the machine learning algorithm to find the underneath relationship of the atomic configuration and energy [128]. ...
... It is of interest to juxtapose the insight that while still sampling the reactant well it is possible to predict whether or not a particular trajectory is likely to react with explicit sampling of reactive vs. non-reactive initial conditions. 146 Analysis of the minimum dynamical path for reactions in the gas phase showed that specific combinations of initial position and momenta in the reactant state lead to reactive trajectories whereas initial conditions outside this manifold do not react. ...
... 186 Using multi state adiabatic reactive dynamics (MS-ARMD) simulations, the transformation from chorismate to prephenate and corresponding smaller molecular systems was investigated. 187 The catalytic effect of the protein over the reaction in water was correctly captured whereas the actual activation free energy did not reproduce that experimentally observed. This can be achieved from using a dedicated parametrization as was done for EVB-based simulations of the same reaction. ...
... The coupled electron-nuclear dynamics in molecules has been studied extensively on the femtosecond timescale, as reviewed for example in Gatti (2014), Bircher et al. (2017), and very recently on the attosecond timescale (Nisoli et al., 2017;Cattaneo et al., 2018). ...
... These motions have to be delineated from larger secondary structure transformations which typically occur on slower timescales between 10 −6 and 10 −3 s. Some examples of these slow changes are allosteric transitions [48,49], cadherin catch bond lifetimes up to 10 −2 s [50], or the spontaneous opening of the integrin on 1 μs timescales [51]. ...
... In this perspective, the selective excitation of the molecular vibrational states represents an effective knob to drive a chemical reaction along a particular pathway [7][8][9]. Moreover, accessing high-lying vibrational states has also proven to enhance the reaction probability in a variety of different systems [10][11][12]. ...
... For larger molecules in the gas phase, MS-ARMD has also been used together with established empirical force fields. This has been applied to the study of specific reaction channels such as proton transfer within H 2 SO 4 or photodissociation of H 2 SO 4 → H 2 O + SO 3 163 and other atmospherically relevant molecules following vibrational excitation of the OH stretch and 164,165 the Claisen rearrangement reaction, 166 or to investigate Diels-Alder reactions. 167 Such studies provide molecular-level details into the reaction mechanisms and relevant coordinates driving the reaction based on dynamics studies, which goes beyond scanning and relaxing the energy function along a minimum energy path. ...