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

Interactive Chemical Reactivity Exploration

Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transition-state structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We employ a haptic pointer device with force-feedback to allow the operator the direct manipulation of structures in three dimensions along with simultaneous perception of the quantum mechanical response upon structure modification as forces. We elaborate on the details of how such an interactive exploration should proceed and which technical difficulties need to be overcome. All reactivity-exploration concepts developed for this purpose have been implemented in the Samson programming environment.Comment: 36 pages, 14 figure

A Robust and Efficient Method for Solving Point Distance Problems by Homotopy

The goal of Point Distance Solving Problems is to find 2D or 3D placements of points knowing distances between some pairs of points. The common guideline is to solve them by a numerical iterative method (\emph{e.g.} Newton-Raphson method). A sole solution is obtained whereas many exist. However the number of solutions can be exponential and methods should provide solutions close to a sketch drawn by the user.Geometric reasoning can help to simplify the underlying system of equations by changing a few equations and triangularizing it.This triangularization is a geometric construction of solutions, called construction plan. We aim at finding several solutions close to the sketch on a one-dimensional path defined by a global parameter-homotopy using a construction plan. Some numerical instabilities may be encountered due to specific geometric configurations. We address this problem by changing on-the-fly the construction plan.Numerical results show that this hybrid method is efficient and robust

Monte Carlo evaluation of the equilibrium isotope effects using the Takahashi-Imada factorization of the Feynman path integral

The Feynman path integral approach for computing equilibrium isotope effects and isotope fractionation corrects the approximations made in standard methods, although at significantly increased computational cost. We describe an accelerated path integral approach based on three ingredients: the fourth- order Takahashi-Imada factorization of the path integral, thermodynamic integration with respect to mass, and centroid virial estimators for relevant free energy derivatives. While the frst ingredient speeds up convergence to the quantum limit, the second and third improve statistical convergence. The combined method is applied to compute the equilibrium constants for isotope exchange reactions H2+D=H+HD and H2+D2=2HD

Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations

We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables. Techniques from traditional numerical analysis (Newton-Raphson, coarse projective integration) are thus enabled; these techniques help analyze important features of the free-energy landscape (coarse transition states, eigenvalues and eigenvectors, transition rates, etc.). Reverse integration of (irreversible) expected coarse variables backward in time can assist escape from free energy minima and trace low-dimensional free energy surfaces. To illustrate the ``coarse molecular dynamics'' approach, we combine multiple short (0.5-ps) replica simulations to map the free energy surface of the ``alanine dipeptide'' in water, and to determine the ~ 1/(1000 ps) rate of interconversion between the two stable configurational basins corresponding to the alpha-helical and extended minima.Comment: The article has been submitted to "The Journal of Chemical Physics.

Computational analysis of single rising bubbles influenced by soluble surfactant

This paper presents novel insights about the influence of soluble surfactants on bubble flows obtained by Direct Numerical Simulation (DNS). Surfactants are amphiphilic compounds which accumulate at fluid interfaces and significantly modify the respective interfacial properties, influencing also the overall dynamics of the flow. With the aid of DNS local quantities like the surfactant distribution on the bubble surface can be accessed for a better understanding of the physical phenomena occurring close to the interface. The core part of the physical model consists in the description of the surfactant transport in the bulk and on the deformable interface. The solution procedure is based on an Arbitrary Lagrangian-Eulerian (ALE) Interface-Tracking method. The existing methodology was enhanced to describe a wider range of physical phenomena. A subgrid-scale (SGS) model is employed in the cases where a fully resolved DNS for the species transport is not feasible due to high mesh resolution requirements and, therefore, high computational costs. After an exhaustive validation of the latest numerical developments, the DNS of single rising bubbles in contaminated solutions is compared to experimental results. The full velocity transients of the rising bubbles, especially the contaminated ones, are correctly reproduced by the DNS. The simulation results are then studied to gain a better understanding of the local bubble dynamics under the effect of soluble surfactant. One of the main insights is that the quasi-steady state of the rise velocity is reached without ad- and desorption being necessarily in local equilibrium

Multiple-scattering effects on incoherent neutron scattering in glasses and viscous liquids

Incoherent neutron scattering experiments are simulated for simple dynamic models: a glass (with a smooth distribution of harmonic vibrations) and a viscous liquid (described by schematic mode-coupling equations). In most situations multiple scattering has little influence upon spectral distributions, but it completely distorts the wavenumber-dependent amplitudes. This explains an anomaly observed in recent experiments

Non-adiabatic effects during the dissociative adsorption of O2 at Ag(111)? A first-principles divide and conquer study

We study the gas-surface dynamics of O2 at Ag(111) with the particular objective to unravel whether electronic non-adiabatic effects are contributing to the experimentally established inertness of the surface with respect to oxygen uptake. We employ a first-principles divide and conquer approach based on an extensive density-functional theory mapping of the adiabatic potential energy surface (PES) along the six O2 molecular degrees of freedom. Neural networks are subsequently used to interpolate this grid data to a continuous representation. The low computational cost with which forces are available from this PES representation allows then for a sufficiently large number of molecular dynamics trajectories to quantitatively determine the very low initial dissociative sticking coefficient at this surface. Already these adiabatic calculations yield dissociation probabilities close to the scattered experimental data. Our analysis shows that this low reactivity is governed by large energy barriers in excess of 1.1 eV very close to the surface. Unfortunately, these adiabatic PES characteristics render the dissociative sticking a rather insensitive quantity with respect to a potential spin or charge non-adiabaticity in the O2-Ag(111) interaction. We correspondingly attribute the remaining deviations between the computed and measured dissociation probabilities primarily to unresolved experimental issues with respect to surface imperfections.Comment: 18 pages including 6 figure