arXiv subjects

Johannes Kästner

Publications and source records attributed to Johannes Kästner.

At least 55 records · Page 3Linked to original sources

arXiv2020

Gaussian Process Regression for Transition State Search

We implemented a gradient-based algorithm for transition state search which uses Gaussian process regression. Besides a description of the algorithm, we provide a method to find the starting point for the optimization if only the reactant and product minima are known. We perform benchmarks on 27 test systems against the dimer method and partitioned rational function optimization as implemented in the DL-FIND library. We found the new optimizer to significantly decrease the number of required energy and gradient evaluations.

physics.chem-ph↗

arXiv2020

Low-Temperature Kinetic Isotope Effects in CH3OH+H -> CH2OH+H2 Shed Light on the Deuteration of Methanol in Space

We calculated reaction rate constants including atom tunneling for the hydrogen abstraction reaction CH3OH+H -> CH2OH+H2 with the instanton method. The potential energy was fitted by a neural network, that was trained to UCCSD(T)-F12/VTZ-F12 data. Bimolecular gas-phase rate constants were calculated using microcanonic instanton theory. All H/D isotope patterns on the CH3 group and the incoming H atom are studied. Unimolecular reaction rate constants, representing the reaction on a surface, down to 30 K, are presented for all isotope patterns. At 30 K they range from 4100 for the replacement of the abstracted H by D to ~ 8 for the replacement of the abstracting H to about 2--6 for secondary KIEs. The $^\text{12}$C/$^\text{13}$C kinetic isotope effect is 1.08 at 30 K, while the $^\text{16}$O/$^\text{18}$O kinetic isotope effect is vanishingly small. A simple kinetic surface model using these data predicts high abundances of the deuterated forms of methanol.

physics.chem-ph↗

arXiv2020

Atom Tunneling in the Hydroxylation Process of Taurine/$α$-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations

TauD dioxygenase is one of the most studied $α$-ketoglutarate dependent dioxygenases ($α$KGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the $α$KGDs, the hydrogen transfer process, by a QM/MM approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe=O cofactor. We found quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5\textcelsius{}. As a consequence a quite high KIE value of close to 60 is obtained, which is consistent with the experimental value.

physics.chem-ph↗

arXiv2020

Comparison of classical reaction paths and tunneling paths studied with the semiclassical instanton theory

Atom tunneling in the hydrogen atom transfer reaction of the 2,4,6-tri-tert-butylphenyl radical to 3,5-di-tert-butylneophyl, which has a short but strongly curved reaction path, was investigated using instanton theory. We found the tunneling path to deviate qualitatively from the classical intrinsic reaction coordinate, the steepest-descent path in mass-weighted Cartesian coordinates. To perform that comparison, we implemented a new variant of the predictor-corrector algorithm for the calculation of the intrinsic reaction coordinate. We used the reaction force analysis method as a means to decompose the reaction barrier into structural and electronic components. Due to the narrow energy barrier, atom tunneling is important in the abovementioned reaction, even above room temperature. Our calculated rate constants between 350 K and 100 K agree well with experimental values. We found a H/D kinetic isotope effect of almost 106 at 100 K. Tunneling dominates the protium transfer below 400 K and the deuterium transfer below 300 K. We compared the lengths of the tunneling path and the classical path for the hydrogen atom transfer in the reaction HCl + Cl and quantified the corner cutting in this reaction. At low temperature, the tunneling path is about 40% shorter than the classical path.

physics.chem-ph↗

arXiv2020

Potential energy surface interpolation with neural networks for instanton rate calculations

Artificial neural networks are used to fit a potential energy surface. We demonstrate the benefits of using not only energies, but also their first and second derivatives as training data for the neural network. This ensures smooth and accurate Hessian surfaces, which are required for rate constant calculations using instanton theory. Our aim was a local, accurate fit rather than a global PES, because instanton theory requires information on the potential only in the close vicinity of the main tunneling path. Elongations along vibrational normal modes at the transition state are used as coordinates for the neural network. The method is applied to the hydrogen abstraction reaction from methanol, calculated on a coupled-cluster level of theory. The reaction is essential in astrochemistry to explain the deuteration of methanol in the interstellar medium.

physics.chem-ph↗

arXiv2020

Vibrational analysis of methyl cation - rare gas atom complexes: CH$_3^+$-Rg (Rg=He, Ne, Ar, Kr)

The vibrational spectra of simple CH$_3^+$-Rg (Rg=He, Ne, Ar, Kr) complexes have been studied by vibrational configuration interaction (VCI) theory relying on multidimensional potential energy surfaces (PES) obtained from explicitly correlated coupled cluster calculations, CCSD(T)-F12a. In agreement with experimental results, the series of rare gas atoms leads to rather unsystematic results and indicates huge zero point vibrational energy effects for the helium complex. In order to study these sensitive complexes more consistently, we also introduce configuration averaged vibrational self-consistent field theory (CAVSCF), which is a generalization of standard VSCF theory to several configurations. The vibrational spectra of the complexes are compared to that of the methyl cation, for which corrections due to scalar-relativistic effects, high-level coupled-cluster terms, i.e. CCSDTQ, and core-valence correlation have explicitly been accounted for. The occurrence of tunneling splittings for the vibrational ground-state of CH$_3^+$-He has been investigated on the basis of semiclassical instanton theory. These calculations and a direct comparison of the energy profiles along the intrinsic reaction coordinates (IRC) with that of the hydronium cation, H$_3$O$^+$, suggest that tunneling effects for vibrationally excited states should be very small.

physics.chem-ph↗

arXiv2020

Tunneling Rate Constants for H2CO+H on Amorphous Solid Water Surfaces

Formaldehyde (H2CO) is one of the most abundant molecules observed in the icy mantle covering interstellar grains. Studying its evolution can contribute to our understanding of the formation of complex organic molecules in various interstellar environments. In this work, we investigated the hydrogenation reactions of H2CO yielding CH3O, CH2OH, and the hydrogen abstraction resulting in H2+HCO on an amorphous solid water (ASW) surface using a quantum mechanics/molecular mechanics (QM/MM) model. The binding energies of H2CO on the ASW surface vary broadly, from 1000 to 9370 K. No correlation was found between binding energies and activation energies of hydrogenation reactions. Combining instanton theory with QM/MM modeling, we calculated rate constants for the Langmuir Hinshelwood and the Eley Rideal mechanisms for the three product channels of H+H2CO surface reactions down to 59 K. We found that the channel producing CH2OH can be ignored, owing to its high activation barrier leading to significantly lower rates than the other two channels. The ASW surface influences the reactivity in favor of formation of CH3O (branching ratio 80%) and hinders the H2CO dissociation into H2+HCO. In addition, kinetic isotope effects are strong in all reaction channels and vary strongly between the channels. Finally, we provide fits of the rate constants to be used in astrochemical models.

astro-ph.GA↗

arXiv2020

Rate constants from instanton theory via a microcanonical approach

Microcanonical instanton theory offers the promise of providing rate constants for chemical reactions including quantum tunneling of atoms over the whole temperature range. We discuss different rate expressions, which require the calculation of stability parameters of the instantons. The traditional way of obtaining these stability parameters is shown to be numerically unstable in practical applications. We provide three alternative algorithms to obtain such stability parameters for non-separable systems, i.e., systems in which the vibrational modes perpendicular to the instanton path couple to movement along the path. We show the applicability of our algorithms on two molecular systems: H$_2$ + OH $\rightarrow$ H$_2$O + H using a fitted potential energy surface and HNCO + H $\rightarrow$ NH$_2$CO using a potential obtained on-the-fly from density functional calculations.

physics.chem-ph↗

arXiv2020

Isomers in Interstellar Environments (I): The Case of Z- and E-Cyanomethanimine

In this work, we present the results of our investigation into the chemistry of Z- and E-cyanomethanimine (HNCHCN), both of which are possible precursors to the nucleobase adenine. Ab initio quantum chemical calculations for a number of reactions with atomic hydrogen were carried out. We find that the reaction H + Z/E-HNCHCN leading both to H-addition as well as H$_2$-abstraction proceed via similar short-range barriers with bimolecular rate coefficients on the order of $\sim10^{-17}$ cm$^{3}$ s$^{-1}$. These results were then incorporated into astrochemical models and used in simulations of the giant molecular cloud G+0.693. The calculated abundances obtained from these models were compared with previous observational data and found to be in good agreement, with a predicted [Z/E] ratio of $\sim3$ - somewhat smaller than the previously derived value of $6.1\pm2.4$. We find that the [Z/E] ratio in our simulations is due mostly to ion-molecule destruction rates driven by the different permanent dipoles of the two conformers. Based on these results, we propose a general rule-of-thumb for estimating the abundances of isomers in interstellar environments.

astro-ph.GA↗

arXiv2020

Efficient Training of ANN Potentials by Including Atomic Forces via Taylor Expansion and Application to Water and a Transition-Metal Oxide

Artificial neural network (ANN) potentials enable the efficient large-scale atomistic modeling of complex materials with near first-principles accuracy. For molecular dynamics simulations, accurate energies and interatomic forces are a prerequisite, but training ANN potentials simultaneously on energies and forces from electronic structure calculations is computationally demanding. Here, we introduce an efficient alternative method for the training of ANN potentials on energy and force information based on an extrapolation of the total energy via a Taylor expansion. By translating the force information to approximate energies, the quadratic scaling with the number of atoms exhibited by conventional force-training methods can be avoided, which enables the training on reference data sets containing complex atomic structures. We demonstrate for different materials systems, clusters of water molecules, bulk liquid water, and a lithium transition-metal oxide, that the proposed force-training approach provides substantial improvements over schemes that train on energies only. Including force information for training reduces the size of the reference data sets required for ANN potential construction, increases the transferability of the potential, and generally improves the force prediction accuracy. For a set of water clusters, the Taylor-expansion approach achieves around 50% of the force error improvement compared to the explicit training on all force components, at a much smaller computational cost. The alternative force training approach thus simplifies the construction of general ANN potentials for the prediction of accurate energies and interatomic forces for diverse types of materials, as demonstrated here for water and a transition-metal oxide.

physics.comp-ph↗

arXiv2019

The role of atom tunneling in gas-phase reactions in planet-forming disks

This paper investigates the impact of the increased reaction rate constant due to tunneling effects on planet-forming disks. Our aim is to quantify the astrophysical implications of atom tunneling for simple molecules that are frequently used to infer disk structure information or to define the initial conditions for planet (atmosphere) formation. We explain the tunneling effect on reaction rates by using a scholarly example in comparison to previous UMIST2012 rate constants. In a chemical network with 1299 reactions, we identify all reactions that could show atom tunneling. We devise a simple formulation of reaction rate constants that overestimates tunneling and screen a standard T Tauri disk model for changes in species abundances. For those reactions found to be relevant, we find values of the most recent literature for the rate constants including tunneling and compare the resulting disk chemistry to the standard disk models. The rate constants in the UMIST2012 database in many cases already capture tunneling effects implicitly. A rigorous screening procedure identified three neutral-neutral reactions where atom tunneling could change simple molecule abundances. However, by adopting recent values of the rate constants of these reactions and due to the layered structure of planet-forming disks, the effects are limited to a small region where cold neutral-neutral chemistry dominates. Abundances of water close to the midplane snowline can increase by a factor of two at most compared to previous results with UMIST2012 rates. Observables from the disk surface, such as high excitation (> 500 K) water line fluxes, decrease by 60% at most when tunneling effects are explicitly excluded. On the other hand, disk midplane quantities relevant for planet formation such as the C-to-O ratio and also the ice-to-rock ratio are clearly affected by these gas-phase tunneling effects.

astro-ph.SR↗

arXiv2019

The Case of H$_2$C$_3$O Isomers, Revisited: Solving the Mystery of the Missing Propadienone

To date, two isomers of H$_2$C$_3$O have been detected, namely, propynal (HCCCHO) and cylclopropenone (c-H$_2$C$_3$O). A third, propadienone (CH$_2$CCO), has thus far eluded observers despite the fact that it is the lowest in energy of the three. This previously noted result is in contradiction of the minimum energy principle, which posits that the abundances of isomers in interstellar environments can be predicted based on their relative stabilities - and suggests, rather, the importance of kinetic over thermodynamic effects in explaining the role of such species. Here, we report results of \textit{ab initio} quantum chemical calculations of the reaction between H and (a) HC$_3$O, (b) H$_2$C$_3$O (both propynal and propadienone), and (c) CH$_2$CHCO. We have found that, among all possible reactions between atomic hydrogen and either propadienone or propynal, only the destruction of propadienone is barrierless and exothermic. That this destruction pathway is indeed behind the non-detection of CH$_2$CCO is further suggested by our finding that the product of this process, the radical CH$_2$CHCO, can subsequently react barrierlessly with H to form propenal (CH$_2$CHCHO) which has, in fact, been detected in regions where the other two H$_2$C$_3$O isomers are observed. Thus, these results not only shed light on a previously unresolved astrochemical mystery, but also further highlight the importance of kinetics in understanding the abundances of interstellar molecules.

astro-ph.GA↗

arXiv2019

Formation of Acetaldehyde on CO-rich Ices

The radicals HCO and CH$_3$ on carbon monoxide ice surfaces were simulated using density functional theory. Their binding energy on amorphous CO ice shows broad distributions, with approximative average values of 500 K for HCO and 200 K for CH$_3$. If they are located on the surface close to each other (3 to 4 Å), molecular dynamics calculations based on density functional theory show that they can form acetaldehyde (CH$_3$CHO) or CH$_4$ + CO in barrier-less reactions, depending on the initial orientation of the molecules with respect to each other. In some orientations, no spontaneous reactions were found, the products remained bound to the surface. Sufficient configurational sampling, inclusion of the vibrational zero point energy, and a thorough benchmark of the applied electronic structure method are important to predict reliable binding energies for such weakly interacting systems. From these results it is clear that complex organic molecules, like acetaldehyde, can be formed by recombination reactions of radicals on CO surfaces.

astro-ph.GA↗

arXiv2017

Tunneling Reaction Kinetics for the Hydrogen Abstraction Reaction H + H$_2$S -> H$_2$ + HS in the Interstellar Medium

The hydrogen abstraction reaction between H and H$_2$S, yielding HS and H$_2$ as products, has been studied within the framework of interstellar surface chemistry. High-temperature rate constants up to 2000 K are calculated in the gas phase and are in agreement with previously reported values. Subsequently low-temperature rate constants down to 55 K are presented for the first time that are of interest to astrochemistry, i.e., covering both bimolecular and unimolecular reaction mechanisms. For this, a so-called implicit surface model is used. Strictly speaking, this is a structural gas-phase model in which the restriction of the rotation in the solid state is taken into account. The calculated kinetic isotope effects are explained in terms of difference in activation and delocalization. All rate constants are calculated at the UCCSD(T)-F12/cc-VTZ-F12 level of theory. Finally, we show that the energetics of the reaction is only affected to a small extent by the presence of H$_2$O or H$_2$S molecular clusters that simulate an ice surface, calculated at the MPWB1K/def2-TZVP level of theory.

astro-ph.GA↗

arXiv2017

Atom Tunneling in the Water Formation Reaction H$_2$ + OH $\rightarrow$ H$_2$O + H on an Ice Surface

OH radicals play a key role as an intermediate in the water formation chemistry of the interstellar medium. For example the reaction of OH radicals with H$_2$ molecules is among the final steps in the astrochemical reaction network starting from O, O$_2$, and O$_3$. Experimentally it was shown that even at 10 K this reaction occurs on ice surfaces. As the reaction has a high activation energy only atom tunneling can explain such experimental findings. In this study we calculated reaction rate constants for the title reaction on a water-ice I$_h$ surface. To our knowledge, low-temperature rate constants on a surface are not available in the literature. All surface calculations were done using a QM/MM framework (BHLYP/TIP3P) after a thorough benchmark of different density functionals and basis sets to highly accurate correlation methods. Reaction rate constants are obtained using instanton theory which takes atom tunneling into account inherently, with constants down to 110 K for the Eley-Rideal mechanism and down to 60 K for the Langmuir-Hinshelwood mechanism. We found that the reaction is nearly temperature independent below 80 K. We give kinetic isotope effects for all possible deuteration patterns for both reaction mechanisms. For the implementation in astrochemical networks, we also give fit parameters to a modified Arrhenius equation. Finally, several different binding sites and binding energies of OH radicals on the I$_h$ surface are discussed and the corresponding rate constants are compared to the gas-phase case.

astro-ph.GA↗

arXiv2017

Influence of surface and bulk water ice on the reactivity of a water-forming reaction

On the surface of icy dust grains in the dense regions of the interstellar medium a rich chemistry can take place. Due to the low temperature, reactions that proceed via a barrier can only take place through tunneling. The reaction H + H$_2$O$_2$ $\rightarrow$ H$_2$O + OH is such a case with a gas-phase barrier of $\sim$26.5 kJ/mol. Still the reaction is known to be involved in water formation on interstellar grains. Here, we investigate the influence of a water ice surface and of bulk ice on the reaction rate constant. Rate constants are calculated using instanton theory down to 74 K. The ice is taken into account via multiscale modeling, describing the reactants and the direct surrounding at the quantum mechanical level with density functional theory (DFT), while the rest of the ice is modeled on the molecular mechanical level with a force field. We find that H$_2$O$_2$ binding energies cannot be captured by a single value, but rather depend on the number of hydrogen bonds with surface molecules. In highly amorphous surroundings the binding site can block the routes of attack and impede the reaction. Furthermore, the activation energies do not correlate with the binding energies of the same sites. The unimolecular rate constants related to the Langmuir-Hinshelwood mechanism increase as the activation energy decreases. Thus, we provide a lower limit for the rate constant and argue that rate constants can have values up to two order of magnitude larger than this limit.

astro-ph.GA↗

arXiv2016

Importance of tunneling in H-abstraction reactions by OH radicals: The case of CH4 + OH studied through isotope-substituted analogs

We present a combined experimental and theoretical study focussing on the quantum tunneling of atoms in the reaction between CH4 and OH. The importance of this reaction pathway is derived by investigating isotope substituted analogs. Quantitative reaction rates needed for astrochemical models at low temperature are currently unavailable both in the solid state and in the gas phase. Here, we study tunneling effects upon hydrogen abstraction in CH4 + OH by focusing on two reactions: CH4 + OD -> CH3 + HDO and CD4 + OH -> CD3 + HDO. The experimental study shows that the solid-state reaction rate R(CH4 + OD) is higher than R(CD4 + OH) at 15 K. Experimental results are accompanied by calculations of the corresponding unimolecular and bimolecular reaction rate constants using instanton theory taking into account surface effects. From the work presented here, the unimolecular reactions are particularly interesting as these provide insight into reactions following a Langmuir-Hinshelwood process. The resulting ratio of the rate constants shows that the H abstraction (k(CH4 + OD)) is approximately ten times faster than D-abstraction (k(CD4 + OH)) at 65 K. We conclude that tunneling is involved at low temperatures in the abstraction reactions studied here. The unimolecular rate constants can be used by the modeling community as a first approach to describe OH-mediated abstraction reactions in the solid phase. For this reason we provide fits of our calculated rate constants that allow the inclusion of these reactions in models in a straightforward fashion.

astro-ph.GA↗

arXiv2016

Quantum tunneling during interstellar surface-catalyzed formation of water: the reaction H + H$_2$O$_2$ $\rightarrow$ H$_2$O + OH

The final step of the water formation network on interstellar grain surfaces starting from the H + O$_2$ route is the reaction between H and H$_2$O$_2$. This reaction is known to have a high activation energy and therefore at low temperatures it can only proceed via tunneling. To date, however, no rate constants are available at temperatures below 200 K. In this work, we use instanton theory to compute rate constants for the title reaction with and without isotopic substitutions down to temperatures of 50 K. The calculations are based on density functional theory, with additional benchmarks for the activation energy using unrestricted single-reference and multireference coupled-cluster single-point energies. Gas-phase bimolecular rate constants are calculated and compared with available experimental data not only for H + H$_2$O$_2$ $\rightarrow$ H$_2$O + OH, but also for H + H$_2$O$_2$ $\rightarrow$ H$_2$ + HO$_2$. We find a branching ratio where the title reaction is favored by at least two orders of magnitude at 114 K. In the interstellar medium this reaction predominantly occurs on water surfaces, which increases the probability that the two reactants meet. To mimic this one, two, or three spectator H2O molecules are added to the system. Eley-Rideal bimolecular and Langmuir-Hinshelwood unimolecular rate constants are presented here. The kinetic isotope effects for the various cases are compared to experimental data as well as to expressions commonly used in astrochemical models. Both the rectangular barrier and the Eckart approximations lead to errors of about an order of magnitude. Finally, fits of the rate constants are provided as input for astrochemical models.

physics.chem-ph↗