arXiv subjects

Markus Meuwly

Publications and source records attributed to Markus Meuwly.

At least 73 records · Page 4Linked to original sources

arXiv2022

Transfer learning for affordable and high quality tunneling splittings from instanton calculations

The combination of transfer learning (TL) a low level potential energy surface (PES) to a higher level of electronic structure theory together with ring-polymer instanton (RPI) theory is explored and applied to malonaldehyde. The RPI approach provides a semiclassical approximation of the tunneling splitting and depends sensitively on the accuracy of the PES. With second order Møller-Plesset perturbation theory (MP2) as the low-level (LL) model and energies and forces from coupled cluster singles, doubles and perturbative triples (CCSD(T)) as the high-level (HL) model, it is demonstrated that CCSD(T) information from only 25 to 50 judiciously selected structures along and around the instanton path suffice to reach HL-accuracy for the tunneling splitting. In addition, the global quality of the HL-PES is demonstrated through a mean average error of 0.3 kcal/mol for energies up to 40 kcal/mol above the minimum energy structure (a factor of 2 higher than the energies employed during TL) and $< 2 $ cm$^{-1}$ for harmonic frequencies compared with computationally challenging normal mode calculations at the CCSD(T) level.

physics.chem-ph↗

arXiv2022

Structure, Organization and Heterogeneity of Water-Containing Deep Eutectic Solvents

The spectroscopy and structural dynamics of a deep eutectic mixture (KSCN/acetamide) with varying water content is investigated from 2D IR (with the C-N stretch vibration of the SCN$^-$ anions as the reporter) and THz spectroscopy. Molecular dynamics simulations correctly describe the non-trivial dependence of both spectroscopic signatures depending on water content. For the 2D IR spectra, the MD simulations relate the steep increase in the cross relaxation rate at high water content to parallel alignment of packed SCN$^-$ anions. Conversely, the non-linear increase of the THz absorption with increasing water content is mainly attributed to the formation of larger water clusters. The results demonstrate that a combination of structure sensitive spectroscopies and molecular dynamics simulations provides molecular-level insights into emergence of heterogeneity of such mixtures by modulating their composition.

physics.chem-ph↗

arXiv2022

Molecular Dynamics with Conformationally Dependent, Distributed Charges

Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their ability to qualitatively and correctly represent chemically significant features such as sigma holes. It has also been shown that off-center point charges offer a compact alternative with similar accuracy. Here it is demonstrated that allowing relocation of charges within a minimally distributed charge model (MDCM) with respect to their reference atoms is a viable route to capture changes in the molecular charge distribution depending on geometry. The approach, referred to as ``flexible MDCM'' (fMDCM) is validated on a number of small molecules and provides accuracies in the electrostatic potential (ESP) of 0.5 kcal/mol on average compared with reference data from electronic structure calculations whereas MDCM and point charges have root mean squared errors of a factor of 2 to 5 higher. In addition, MD simulations in the $NVE$ ensemble using fMDCM for a box of flexible water molecules with periodic boundary conditions show a width of 0.1 kcal/mol for the fluctuation around the mean at 300 K on the 10 ns time scale. The accuracy in capturing the geometry dependence of the ESP together with the long-time stability in energy conserving simulations makes fMDCM a promising tool to introduce advanced electrostatics into atomistic simulations.

physics.chem-ph↗

arXiv2022

Quantum and Quasi-classical Dynamics of the C($^{3}$P) + O$_{2}$($^3Σ_{g}^{-}$) $\rightarrow$ CO($^{1}Σ^{+}$)+ O($^{1}$D) Reaction on Its Electronic Ground State

The dynamics of the C($^{3}$P) + O$_{2}$($^3Σ_{g}^{-}$) $\rightarrow$ CO($^{1}Σ^{+}$)+ O($^{1}$D) reaction on its electronic ground state is investigated by using time-dependent wave packet propagation (TDWP) and quasi-classical trajectory (QCT) simulations. For the moderate collision energies considered ($E_{\rm c} = 0.001$ to 0.4 eV, corresponding to a range from 10 K to 4600 K) the total reaction probabilities from the two different treatments of the nuclear dynamics agree very favourably. The undulations present in $P(E)$ from the quantum mechanical treatment can be related to stabilization of the intermediate CO$_2$ complex with lifetimes of on the 0.05 ps time scale. This is also confirmed from direct analysis of the QCT trajectories. Product diatom vibrational and rotational level resolved state-to-state reaction probabilities from TDWP and QCT simulations also agree well except for the highest product vibrational states $(v' \geq 15)$ and for the lowest product rotational states $(j' \leq 10)$. Opening of the product vibrational level CO$(v' = 17)$ requires $\sim 0.2$ eV from QCT and TDWP simulations with O$_2$($j=0$) and decreases to 0.04 eV if all initial rotational states are included in the QCT analysis, compared with $E_{\rm c} > 0.04$ eV obtained from experiments. It is thus concluded that QCT simulations are suitable for investigating and realistically describe the C($^{3}$P) + O$_{2}$($^3Σ_{g}^{-}$) $\rightarrow$ CO($^{1}Σ^{+}$)+ O($^{1}$D) reaction down to low collision energies when compared with results from a quantum mechanical treatment using TDWPs.

physics.chem-ph↗

arXiv2022

Hydration Dynamics and IR Spectroscopy of 4-Fluorophenol

Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of $para$-fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine-Learning (ML) based parametrization and with full $\textit{ab initio}$ (QM) and mixed Quantum Mechanical/Molecular Mechanics (QM/MM) simulations with a particular focus on the CF- and OH-stretch region. The CF-stretch band is heavily mixed with other modes whereas the OH-stretch in solution displays a characteristic high-frequency peak around 3600 cm$^{-1}$ most likely associated with the -OH group of PhOH and F-PhOH together with a characteristic progression below 3000 cm$^{-1}$ due to coupling with water modes which is also reproduced by several of the simulations. Solvent and radial distribution functions indicate that the CF-site is largely hydrophobic except for simulations using point charges which renders them unsuited for correctly describing hydration and dynamics around fluorinated sites.

physics.chem-ph↗

arXiv2022

Double Proton Transfer in Hydrated Formic Acid Dimer: Interplay of Spatial Symmetry and Solvent-Generated Force on Reactivity

The double proton transfer (DPT) reaction in hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed - as in a conventional empirical force field - and conformationally fluctuating - as available from the ML-based PES - charge models for FAD shows significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% ($\sim 1$ kcal/mol) between 300 K and 600 K. The rate for DPT is largest, $\sim 1$ ns$^{-1}$, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O-H$\cdots$O hydrogen bond whereas the second proton transfer is significantly controlled by the O-O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors.

physics.chem-ph↗

arXiv2022

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 empirical energy functions, machine-learned force fields, and methods that separate sampling conformational space and determining the data for spectral analysis such as map-based approaches.

physics.chem-ph↗

arXiv2022

Photodissociation dynamics of N$_{3}^{+}$

The photodissociation dynamics of N$_3^+$ excited from its $^3 Σ_{\rm g}^{-}$ ground to the first excited singlet and triplet states is investigated. Three dimensional potential energy surfaces for the $^1$A$'$, $^1$A$''$, and $^3$A$'$ electronic states, correlating with the $^1 Δ_{\rm g}$ and $^3 Π_{\rm u}$ states in linear geometry, for N$_3^+$ are constructed using high level electronic structure calculations and represented as reproducing kernels. The reference {\it ab initio} energies are calculated at the MRCI+Q/aug-cc-pVTZ level of theory. For following the photodissociation dynamics in the excited states, rotational and vibrational distributions $P(v')$ and $P(j')$ for the N$_2$ product are determined from vertically excited ground state distributions. Due to the different shapes of the ground state $^3$A$^{''}$ PES and the excited states, appreciable angular momentum $j' \sim 60$ is generated in the diatomic fragments. The lifetimes in the excited states extend to at least 50 ps. Notably, results from sampling initial conditions from a thermal ensemble and from the Wigner distribution of the ground state wavefunction are comparable.

physics.chem-ph↗

arXiv2021

Energy Redistribution following CO$_2$ 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 CO$_2$ formed within and on the surface of amorphous solid water (ASW) and the surrounding water is studied. Following CO($^1 Σ^+$) + O($^1$D) recombination the average translational and internal energy of the water molecules increases on the $\sim 10$ ps time scale by 15 % to 20 % depending on whether the reaction takes place on the surface or in an internal cavity of ASW. Due to tight coupling between CO$_2$ 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 $\sim 10$ ps and a considerably slower $\sim 1$ 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 products generated.

physics.chem-ph↗

arXiv2021

Cross-Correlated Motions in Azidolysozyme

The changes in the local and global dynamics of azide-labelled Lysozyme compared with that of the wild type protein are quantitatively assessed for all alanine residues along the polypeptide chain. Although attaching -N$_3$ to alanine residues has been considered to be a minimally invasive change in the protein it is found that depending on the location of the Alanine residue the local and global changes in the dynamics differ. For Ala92 the change in the cross correlated motions are minimal whereas attaching -N$_3$ to Ala90 leads to pronounced differences in the local and global correlations as quantified by cross correlation coefficients of the C$_α$ atoms. It is also demonstrated that the spectral region of the asymmetric azide stretch distinguishes between alanine attachment sites whereas changes in the low frequency, far-infrared region are less characteristic.

physics.chem-ph↗

arXiv2021

Solvent Effects on the Menshutkin Reaction

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 dynamics simulations. For polar solvents (water, methanol, and acetonitrile) and benzene, strong to moderate catalytic effect for both reactions is found whereas apolar and bulky cyclohexane interacts weakly with the solute and does not show pronounced barrier reduction. Calculated barrier heights for the Pyr+MeBr reaction in acetonitrile and cyclohexane are 23.2 and 28.1 kcal/mol compared with experimentally measured barriers of 22.5 and 27.6 kcal/mol, respectively. The 2-dimensional solvent distributions change considerably between reactant and TS but comparatively little between TS and product conformations of the solute. The simulations also suggest that as the system approaches the transition state, correlated solvent motions that destabilize the solvent-solvent interactions are required to surmount the barrier. Finally, the average solvent-solvent interaction energies in the reactant, TS, and product state geometries are correlated with changes in the solvent structure around the solute.

physics.chem-ph↗

arXiv2021

Machine Learning Product State Distributions from Initial Reactant States for a Reactive Atom-Diatom Collision System

A machine learned (ML) model for predicting product state distributions from specific initial states (state-to-distribution or STD) for reactive atom-diatom collisions is presented and quantitatively tested for the N($^4$S)+O$_{2}$(X$^3 Σ_{\rm g}^{-}$) $\rightarrow$ NO(X$^2Π$) +O($^3$P) reaction. The reference data set for training the neural network (NN) consists of final state distributions determined from explicit quasi-classical trajectory (QCT) simulations for $\sim 2000$ initial conditions. Overall, the prediction accuracy as quantified by the root-mean-squared difference $(\sim 0.003)$ and the $R^2$ $(\sim 0.99)$ between the reference QCT and predictions of the STD model is high for the test set and off-grid state specific initial conditions and for initial conditions drawn from reactant state distributions characterized by translational, rotational and vibrational temperatures. Compared with a more coarse grained distribution-to-distribution (DTD) model evaluated on the same initial state distributions, the STD model shows comparable performance with the additional benefit of the state resolution in the reactant preparation. Starting from specific initial states also leads to a more diverse range of final state distributions which requires a more expressive neural network to be used compared with DTD. Direct comparison between explicit QCT simulations, the STD model, and the widely used Larsen-Borgnakke (LB) model shows that the STD model is quantitative whereas the LB model is qualitative at best for rotational distributions $P(j')$ and fails for vibrational distributions $P(v')$. As such the STD model can be well-suited for simulating nonequilibrium high-speed flows, e.g., using the direct simulation Monte Carlo method.

physics.chem-ph↗

arXiv2021

The Functional Role of the Hemoglobin-Water Interface

The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are summarized and put into perspective. One of the main findings from the computations is that the stability of the deoxy, ligand-free T-state (T$_0$) can be stabilized relative to the deoxy R-state (R$_0$) only in sufficiently large simulation boxes for the hydrophobic effect to manifest itself. This effect directly influences protein stability and is operative also under physiological conditions. Furthermore, molecular simulations provide a dynamical interpretation of the Perutz model for Hb function. Results from experiments using higher protein concentrations and realistic cellular environments are also discussed. One of the next great challenges for computational studies, which as we show is likely to be taken up in the near future, is to provide molecular-level understanding of the dynamics of proteins in such crowded environments.

physics.chem-ph↗

arXiv2021

Transfer Learned Potential Energy Surfaces: Accurate Anharmonic Vibrational Dynamics and Dissociation Energies for the Formic Acid Monomer and Dimer

The vibrational dynamics of formic acid monomer (FAM) and dimer (FAD) is investigated from machine-learned potential energy surfaces at the MP2 (PES$_{\rm MP2}$) and transfer-learned (PES$_{\rm TL}$) to the CCSD(T) levels of theory. The normal modes and anharmonic frequencies of all modes below 2000 cm$^{-1}$ agree favourably with experiment whereas the OH-stretch mode is challenging for FAM and FAD from normal mode analyses and finite-temperature MD simulations. VPT2 calculations on PES$_{\rm TL}$ for FAM reproduce the experimental OH frequency to within 22 cm$^{-1}$. For FAD the VPT2 calculations find the high-frequency OH stretch at 3011cm$^{-1}$, compared with an experimentally reported, broad ($\sim 100$ cm$^{-1}$) absorption band with center frequency estimated at $\sim 3050$ cm$^{-1}$. In agreement with earlier reports, MD simulations at higher temperature shift the position of the OH-stretch in FAM to the red, consistent with improved sampling of the anharmonic regions of the PES. However, for FAD the OH-stretch shifts to the blue and for temperatures higher than 1000 K the dimer partly or fully dissociates using PES$_{\rm TL}$. Including zero-point energy corrections from diffusion Monte Carlo simulations for FAM and FAD and corrections due to basis set superposition and completeness errors yield a dissociation energy of $D_0 = -14.23 \pm 0.08$ kcal/mol compared with an experimentally determined value of $-14.22 \pm 0.12$ kcal/mol.

physics.chem-ph↗

arXiv2021

Site-Selective Dynamics of Ligand-Free and Ligand-Bound Azidolysozyme

Azido-modified alanine residues (AlaN$_3$) are environment-sensitive, minimally invasive infrared probes for the site-specific investigation of protein structure and dynamics. Here, the capability of the label is investigated to query whether or not a ligand is bound to the active site of Lysozyme and how the spectroscopy and dynamics change upon ligand binding. The results demonstrate specific differences for center frequencies of the asymmetric azide stretch vibration, the long time decay and the static offset of the frequency fluctuation correlation function - all of which are experimental observables - between the ligand-free and the ligand-bound, N$_3$-labelled protein. Changes in dynamics can also be mapped onto changes in the local and through-space coupling between residues by virtue of dynamical cross-correlation maps. This makes the azide label a versatile and structurally sensitive probe to report on the dynamics of proteins in a variety of environments and for a range of different applications.

physics.bio-ph↗

arXiv2021

Thermal and Vibrationally Activated Decomposition of the syn-CH$_3$CHOO Criegee Intermediate

The full reaction pathway between the syn-CH$_3$CHOO Criegee Intermediate via vinyl hydroxyperoxide to OH+CH$_2$COH is followed for vibrationally excited and thermally prepared reactants. The rates from vibrational excitation are consistent with those found from experiments and tunneling is not required for reactivity at all initial conditions probed. For vibrationally excited reactant, VHP accumulates and becomes a bottleneck for the reaction. The two preparations - relevant for laboratory studies and conditions in the atmosphere - lead to a difference of close to one order of magnitude in OH production (~ 5 % vs. 35 %) on the 1 ns time scale which is an important determinant for the chemical evolution of the atmosphere.

physics.chem-ph↗

arXiv2021

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine-Trimer

The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution is characterized from molecular dynamics (MD) simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1-d infrared spectra, the frequency splitting between the two amide-I groups is 10 cm$^{-1}$ from the PC, 13 cm$^{-1}$ from the MTP, and 47 cm$^{-1}$ from SCC-DFTB simulations, compared with 25 cm$^{-1}$ from experiment. The frequency trajectory required for determining the frequency fluctuation correlation function (FFCF) is determined from individual (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF $C(t=0)$, and the static component $Δ_0^2$ from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)$_3$. Contrary to that, for the analysis excluding mode-mode coupling (INM) the FFCF decays to zero too rapidly and for simulations with a PC-based force field the $Δ_0^2$ is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature , whereas that covered by the MTP-based simulations is dominated by P$_{\rm II}$ which agrees with and confirms recently reported, Bayesian-refined populations based on 1-dimensional infrared experiments. Full normal mode analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.

physics.bio-ph↗

arXiv2021

Genesis of Polyatomic Molecules in Dark Clouds: CO$_2$ Formation on Cold Amorphous Solid Water

Understanding the formation of molecules under conditions relevant to interstellar chemistry is fundamental to characterize the chemical evolution of the universe. Using reactive molecular dynamics simulations with model-based or high-quality potential energy surfaces provides a means to specifically and quantitatively probe individual reaction channels at a molecular level. The formation of CO$_2$ from collision of CO($^1 Σ$) and O($^1$D) is characterized on amorphous solid water (ASW) under conditions typical in cold molecular clouds. Recombination takes place on the sub-nanosecond time scale and internal energy redistribution leads to stabilization of the product with CO$_2$ remaining adsorbed on the ASW on extended time scales. Using a high-level, reproducing kernel-based potential energy surface for CO$_2$, formation into and stabilization of CO$_2$ and COO is observed.

physics.chem-ph↗