Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching

Solving the OH + Glyoxal Problem: A Complete Theoretical Description of Post-Transition-State Energy Deposition in Activated Systems

Activated chemistry in coupled reaction systems has broadened our understanding of the chemical kinetics. In the case of intermediates formed in gas phase abstraction reactions (e.g., OH + HC(O)C(O)H (glyoxal) →HC(O)CO + H2O), it is particularly crucial to understand how the reaction energy is partitioned between product species as this determines the propensity for a given product to undergo "prompt" dissociation (e.g., HC(O)CO → HCO + CO) before the excess reaction energy is removed. An example of such an activated system is the OH + glyoxal + O2 coupled reaction system. In this work, we develop a molecular dynamics pipeline, which, combined with a master equation analysis, accurately models previous experimental measurements. This new work resolves previous complexities and discrepancies from earlier master equation modeling for this reaction system. The detailed molecular dynamics approach employed here is a powerful new tool for modeling challenging activated reaction systems.

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

RATIONALE

Cytosine and its conjugates are prone to form protonated, triply-bonded dimers. Therefore, the nucleic-acid cytosine-rich sequence forms the four-stranded noncanonical secondary structure known as the intercalated motif (i-motif). This process has resulted in studies on cytosine protonated dimers. This communication focuses on the protonated dimers of cytosine and its nucleoside using the survival yield (SY) method and quantum mechanics calculations.

METHODS

To obtain the precursor ion fragmentation curve, the plot of SY against Ecomδ , the product ion spectra of the protonated dimers were obtained using a Waters/Micromass Q-TOF Premier mass spectrometer. Quantum mechanics calculations were performed using GAUSSIAN 16, and full geometry optimizations and energy calculations were performed within the density functional theory framework at B3LYP/6-31G(d,p).

RESULTS

The precursor ion fragmentation curve allowed the rating of the gas-phase stabilities of the analyzed protonated dimers. Substitution of sugar moiety at N1 cytosine atom decreased the gas-phase stabilities of the protonated dimers. The deoxycytidine dimer was found to be more stable than the cytidine dimer and cytidine-deoxycytidine dimer. Quantum chemical calculations indicated that cytosine aminohydroxy tautomer may be involved in the formation of protonated cytosine-cytosine nucleoside dimers but not in the formation of cytosine dimers.

CONCLUSIONS

The results obtained for nucleoside dimers indicated that the SY method may reflect the i-motif stabilities observed under physiological conditions. Therefore, the analysis of other protonated dimers of variously substituted cytosine-cytosine nucleoside using the SY method may be important to study the effect of cytosine substitution on the i-motif stabilities. Cytosine tautomer containing C2-OH… N(2H)-C4 moiety may be involved in the formation of protonated cytosine-cytosine nucleoside dimers.

Nonadiabatic Kinetics in the Intermediate Coupling Regime: Comparing Molecular Dynamics to an Energy-Grained Master Equation

We propose and test an extension of the energy-grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional relaxation and kinetic processes which transfer population between different electronic states of the same spin symmetry. By incorporating Zhu-Nakamura theory into the EGME, we are able to treat NA passages beyond the simple Landau-Zener approximation, along with the corresponding treatments of zero-point energy and tunneling probability. To evaluate the performance of this NA-EGME approach, we carried out detailed studies of the UV photodynamics of the volatile organic compound C₆-hydroperoxy aldehyde (C₆-HPALD) using on-the-fly ab initio molecular dynamics and trajectory surface hopping. For this multichromophore molecule, we show that the EGME is able to capture important aspects of the dynamics, including kinetic timescales, and diabatic trapping. Such an approach provides a promising and efficient strategy for treating the long-time dynamics of photoexcited molecules in regimes which are difficult to capture using atomistic on-the-fly molecular dynamics.

Vibrational Energy Relaxation of Deuterium Fluoride in d-Dichloromethane: Insights from Different Potentials

Vibrationally excited deuterium fluoride (DF) formed by fluorine atom reaction with a solvent was found (Science, 2015, 347, 530) to relax rapidly (less than 10 ps) in acetonitrile-d₃ (CD₃CN) and dichloromethane-d₂ (CD₂Cl₂). However, insights into how CD₂Cl₂ facilitates this energy relaxation have so far been lacking, given the weak interaction between DF and a single CD₂Cl₂. In this work, we report the results of reactive simulations with a two-state reactive empirical valence bond (EVB) potential to study the energy deposited into nascent DF after transition-state passage and of nonequilibrium molecular dynamics simulations using multiple different potential energy functions to model the relaxation dynamics. For these second simulations, we used the standard Merck molecular force field (MMFF) potential, an MMFF-based covalent-ionic empirical valence bond (EVB) potential (EVB^CI), a newly developed potential [referred to as MMFF(rDF)] which extends upon the MMFF potential by making the DF/CD₂Cl₂ interaction depend on the value of the D-F bond stretching coordinate and by taking the anisotropic charge distribution of the solvent molecules into account, the polarizable atomic multipole optimized energetics for biomolecular applications (AMOEBA) potential, and the quantum mechanics/molecular mechanics (QM/MM) potential. The relaxation is revealed to be highly sensitive to the potential used. Neither standard MMFF nor EVB^CI reproduces the experimentally observed rapid relaxation dynamics, and they also fail to provide a good description of the interaction potential between DF and CD₂Cl₂ as calculated using CCSD(T)-F12. This is attributed to the use of a point-charge model for the solute and to failing to model the anisotropic electrostatic properties of CD₂Cl₂. The MMFF(rDF), AMOEBA, and QM/MM potentials all reproduce the CCSD(T)-F12 two-body DF---CD₂Cl₂ interaction potential rather well but only with the QM/MM approach is fast vibrational relaxation obtained (lifetimes of ∼288, ∼186, and ∼8 ps, respectively), which we attribute to differences in the solute-solvent local structure. With QM/MM, a unique "many-body" interaction pattern in which DF is in close contact with two solvent Cl atoms and more than three solvent D atoms is found, but this structure is not seen with other potentials. The QM/MM dynamics also display enhanced solute-solvent interactions with vibrationally excited DF that induce a DF band redshift and hence a resonant overlap with solvent C-D modes, which facilitate the intermolecular energy transfer. Our work also suggests that potentials used to model energy relaxation need to capture the fine structure of solute-solvent interactions and not just the two-body part.

Exploring Energy Profiles of Protein-Protein Interactions (PPIs) Using DFT Method

Background:

Large-scale energy landscape characterization of protein-protein interactions (PPIs) is important to understand the interaction mechanism and protein-protein docking methods. The experimental methods for detecting energy landscapes are tedious and the existing computational methods require longer simulation time.

Objective:

The objective of the present work is to ascertain the energy profiles at the interface regions in a rapid manner to analyze the energy landscape of protein-protein interactions.

Methods:

The atomic coordinates obtained from the X-ray and NMR spectroscopy data are considered as inputs to compute cumulative energy profiles for experimentally validated protein-protein complexes. The energies computed by the program were comparable to the standard molecular dynamics simulations.

Results:

The PPI Profiler not only enables rapid generation of energy profiles but also facilitates the detection of hot spot residue atoms involved therein.

Conclusion:

The hotspot residues and their computed energies matched with the experimentally determined hot spot residues and their energies which correlated well by employing the MM/GBSA method. The proposed method can be employed to scan entire proteomes across species at an atomic level to study the key PPI interactions.

Molecular dynamics of combustion reactions in supercritical carbon dioxide. Part 4: boxed MD study of formyl radical dissociation and recombination

Fossil fuel oxy-combustion is an emergent technology where habitual nitrogen diluent is replaced by high pressure (supercritical) carbon dioxide. The supercritical state of CO₂ increases the efficiency of the energy conversion and the absence of nitrogen from the reaction mixture reduces pollution by NO_x. However, the effects of a supercritical environment on elementary reactions kinetics are not well understood at present. We used boxed molecular dynamics simulations at the QM/MM theory level to predict the kinetics of dissociation/recombination reaction HCO^• + [M] ↔ H^• + CO + [M], an important elementary step in many combustion processes. A wide range of temperatures (400-1600 K) and pressures (0.3-1000 atm) were studied. Potentials of mean force were plotted and used to predict activation free energies and rate constants. Based on the data obtained, extended Arrhenius equation parameters were fitted and tabulated. The apparent activation energy for the recombination reaction becomes negative above 30 atm. As the temperature increased, the pressure effect on the rate constant decreased. While at 400 K the pressure increase from 0.3 atm to 300 atm accelerated the dissociation reaction by a factor of 250, at 1600 K the same pressure increase accelerated this reaction by a factor of 100. Graphical abstract Formyl radical surrounded by carbon dioxide molecules.

Methyl group transfer upon gas phase decomposition of protonated methyl benzoate and similar compounds

Gas phase decompositions of protonated methyl benzoate and its conjugates have been studied by using electrospray ionization-collision induced dissociation-tandem mass spectrometry. Loss of CO₂ molecule, thus transfer of methyl group, has been observed. In order to better understand this process, the theoretical calculations have been performed. For methyl benzoate conjugates, it has been found that position of substituent affects the loss of CO₂ molecule, not the electron donor/withdrawing properties of the substituent. Therefore, electrospray ionization-mass spectrometry in positive ion mode may be useful for differentiation of isomers of methyl benzoate conjugates.

Molecular dynamics simulations of energy dissipation and non-thermal diffusion on amorphous solid water

Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. Especially, saturated, hydrogen-rich molecules are formed through surface chemistry where the interstellar grains act as a meeting place and absorbing energy. Here we present the results of thousands of molecular dynamics simulations to quantify the outcome of an energy dissipation process. Admolecules on top of an amorphous solid water surface have been given translational energy between 0.5 and 5 eV. Three different surface species are considered, CO₂, H₂O and CH₄, spanning a range in binding energies, number of internal degrees of freedom and molecular weight. The results are compared against a previous study using a crystalline water ice surface. Possible outcomes of a dissipation process are adsorption - possibly after long-range diffusion-, desorption and desorption of a surface molecule. The three admolecules were found to bind at different locations on the surface, particularly in terms of height. Water preferably binds on top of the surface, whereas methane fills the nanopores on the surface. This has direct consequences for desorption, travelled distance, and kick-out probabilities. The admolecules are found to frequently travel several tens of angstroms before stabilizing on a binding site, allowing follow-up reactions en route. We present kick-out probabilities and we have been able to quantify the desorption probability which depends on the binding energy of the species, the translational excitation, and a factor that accounts for difference in binding site height. We provide expressions that can be incorporated in astrochemical models to predict grain surface formation and return into the gas phase of these products.

Failure and Redemption of Statistical and Nonstatistical Rate Theories in the Hydroboration of Alkenes

Our previous work found that canonical forms of transition state theory incorrectly predict the regioselectivity of the hydroboration of propene with BH3 in solution. In response, it has been suggested that alternative statistical and nonstatistical rate theories can adequately account for the selectivity. This paper uses a combination of experimental and theoretical studies to critically evaluate the ability of these rate theories, as well as dynamic trajectories and newly developed localized statistical models, to predict quantitative selectivities and qualitative trends in hydroborations on a broader scale. The hydroboration of a series of terminally substituted alkenes with BH3 was examined experimentally, and a classically unexpected trend is that the selectivity increases as the alkyl chain is lengthened far from the reactive centers. Conventional and variational transition state theories can predict neither the selectivities nor the trends. The canonical competitive nonstatistical model makes somewhat better predictions for some alkenes but fails to predict trends, and it performs poorly with an alkene chosen to test a specific prediction of the model. Added nonstatistical corrections to this model make the predictions worse. Parametrized Rice-Ramsperger-Kassel-Marcus (RRKM)-master equation calculations correctly predict the direction of the trend in selectivity versus alkene size but overpredict its magnitude, and the selectivity with large alkenes remains unpredictable with any parametrization. Trajectory studies in explicit solvent can predict selectivities without parametrization but are impractical for predicting small changes in selectivity. From a lifetime and energy analysis of the trajectories, "localized RRKM-ME" and "competitive localized noncanonical" rate models are suggested as steps toward a general model. These provide the best predictions of the experimental observations and insight into the selectivities.

Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving the quality of potential energy surfaces. In particular, the possibility of using quantum chemistry to calculate energies and forces 'on the fly' has paved the way to directly study chemical reactions. This has provided a valuable tool to explore molecular mechanisms at given temperatures and energies and to see whether these reactive trajectories follow statistical laws and/or minimum energy pathways. This themed issue collects different aspects of the problem and gives an overview of recent works and developments in different contexts, from the gas phase to the condensed phase to excited states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.