Higher order multipole moments for molecular dynamics simulations

In conventional force fields, the electrostatic potential is represented by atom-centred point charges. This choice is in principle arbitrary, but technically convenient. Point charges can be understood as the first term of multipole expansions, which converge with an increasing number of terms towards the accurate representation of the molecular potential given by the electron density distribution. The use of multipole expansions can therefore improve the force field accuracy. Technically, the implementation of atomic multipoles is more involved than the use of point charges. Important points to consider are the orientation of the multipole moments during the trajectory, conformational dependence of the atomic moments and stability of the simulations which are discussed her

Ligand and interfacial dynamics in a homodimeric hemoglobin

The structural dynamics of dimeric hemoglobin (HbI) from Scapharca inaequivalvis in different ligand-binding states is studied from atomistic simulations on the μs time scale. The intermediates are between the fully ligand-bound (R) and ligand-free (T) states. Tertiary structural changes, such as rotation of the side chain of Phe97, breaking of the Lys96-heme salt bridge, and the Fe-Fe separation, are characterized and the water dynamics along the R-T transition is analyzed. All these properties for the intermediates are bracketed by those determined experimentally for the fully ligand-bound and ligand-free proteins, respectively. The dynamics of the two monomers is asymmetric on the 100 ns timescale. Several spontaneous rotations of the Phe97 side chain are observed which suggest a typical time scale of 50-100 ns for this process. Ligand migration pathways include regions between the B/G and C/G helices and, if observed, take place in the 100 ns time scale

Machine Learning for Observables: Reactant to Product State Distributions for Atom-Diatom Collisions

Machine learning-based models to predict product state distributions from a distribution of reactant conditions for atom-diatom collisions are presented and quantitatively tested. The models are based on function-, kernel- and grid-based representations of the reactant and product state distributions. While all three methods predict final state distributions from explicit quasi-classical trajectory simulations with R$^2$ > 0.998, the grid-based approach performs best. Although a function-based approach is found to be more than two times better in computational performance, the kernel- and grid-based approaches are preferred in terms of prediction accuracy, practicability and generality. The function-based approach also suffers from lacking a general set of model functions. Applications of the grid-based approach to nonequilibrium, multi-temperature initial state distributions are presented, a situation common to energy distributions in hypersonic flows. The role of such models in Direct Simulation Monte Carlo and computational fluid dynamics simulations is also discussed

Theoretical and Computational Chemistry

Computer-based and theoretical approaches to chemical problems can provide atomistic understanding of complex processes at the molecular level. Examples ranging from rates of ligand-binding reactions in proteins to structural and energetic investigations of diastereomers relevant to organo-catalysis are discussed in the following. They highlight the range of application of theoretical and computational methods to current questions in chemical research

Collision-induced rotational excitation in N2 (+)((2)Σg (+),v=0)-Ar: Comparison of computations and experiment

The collisional dynamics of N2 (+)((2)Σg (+)) cations with Ar atoms is studied using quasi-classical simulations. N2 (+)-Ar is a proxy to study cooling of molecular ions and interesting in its own right for molecule-to-atom charge transfer reactions. An accurate potential energy surface (PES) is constructed from a reproducing kernel Hilbert space (RKHS) interpolation based on high-level ab initio data. The global PES including the asymptotics is fully treated within the realm of RKHS. From several ten thousand trajectories, the final state distribution of the rotational quantum number of N2 (+) after collision with Ar is determined. Contrary to the interpretation of previous experiments which indicate that up to 98% of collisions are elastic and conserve the quantum state, the present simulations find a considerably larger number of inelastic collisions which supports more recent findings

Computational Vibrational Spectroscopy

Vibrational spectroscopy is a powerful technique to characterize the near-equilibrium dynamics of molecules in the gas and the condensed phase. This contribution summarizes efforts from computer-based methods to gain insight into the relationship between structure and spectroscopic response. Methods for this purpose include physics-based and machine-learned energy functions, and methods that separate sampling conformational space and determining the data for spectral analysis such as map-based techniques

Energy Redistribution following CO2 Formation on Cold Amorphous Solid Water

The formation of molecules in and on amorphous solid water (ASW) as it occurs in interstellar space releases appreciable amounts of energy that need to be dissipated to the environment. Here, energy transfer between CO2 formed within and on the surface of amorphous solid water (ASW) and the surrounding water is studied. Following CO(1Σ+) + O(1D) recombination the average translational and internal energy of the water molecules increases on the ∼10 ps time scale by 15–25% depending on whether the reaction takes place on the surface or in an internal cavity of ASW. Due to tight coupling between CO2 and the surrounding water molecules the internal energy exhibits a peak at early times which is present for recombination on the surface but absent for the process inside ASW. Energy transfer to the water molecules is characterized by a rapid ∼10 ps and a considerably slower ∼1 ns component. Within 50 ps a mostly uniform temperature increase of the ASW across the entire surface is found. The results suggest that energy transfer between a molecule formed on and within ASW is efficient and helps to stabilize the reaction products generated

CO2_2 and NO2_2 Formation on Amorphous Solid Water

The dynamics for molecule formation, relaxation, diffusion, and desorption on amorphous solid water is studied in a quantitative fashion. We aim at characterizing, at a quantitative level, the formation probability, stabilization, energy relaxation and diffusion dynamics of CO$_2$ and NO$_2$ on cold amorphous solid water following atom+diatom recombination reactions. Accurate machine-learned energy functions combined with fluctuating charge models were used to investigate the diffusion, interactions, and recombination dynamics of atomic oxygen with CO and NO on amorphous solid water (ASW). Energy relaxation to the ASW and into water-internal-degrees of freedom were determined from analysis of the vibrational density of states. The surface diffusion and desorption energetics was investigated from extended and nonequilibrium MD simulations. The reaction probability on the nanosecond time scale is determined in a quantitative fashion and demonstrates that surface diffusion of the reactants leads to recombination for initial separations up to 20 \AA\/. After recombination both, CO$_2$ and NO$_2$, stabilize by energy transfer to water internal and surface phonon modes on the picosecond time scale. The average diffusion barriers and desorption energies agree with those reported from experiments. After recombination, the triatomic products diffuse easily which contrasts with the equilibrium situation in which both, CO$_2$ and NO$_2$, are stationary on the multi-nanosecond time scale.Comment: 37 page

Numerical Accuracy Matters: Applications of Machine Learned Potential Energy Surfaces

The role of numerical accuracy in training and evaluating neural network-based potential energy surfaces is examined for different experimental observables. For observables that require third- and fourth-order derivatives of the total energy with respect to Cartesian coordinates single-precision arithmetics as is typically used in ML-based approaches is insufficient and leads to roughness of the underlying PES as is explicitly demonstrated. Increasing the numerical accuracy to double-precision yields a smooth PES with higher-order derivatives that are numerically stable and yield meaningful anharmonic frequencies and tunneling splitting as is demonstrated for H$_2$CO and malonaldehyde. For molecular dynamics simulations, which only require first-order derivatives, single-precision arithmetics appears to be sufficient, though