Theoretical study of NH3 , H2 S, and HCN adsorption enhancement on defective graphene-supported Cu19 clusters.

Recent studies have shown that graphene-supported metal clusters can enhance catalytic reactivity compared with corresponding metal clusters. In this study, the adsorptions of NH3 , H2 S, and HCN on Cu19 and defective graphene-supported Cu19 clusters are investigated using plane-wave density functional theory. The results reveal the three gas molecules can be adsorbed on three types of top sites of Cu atoms, respectively. The adsorption energies of the corresponding adsorption sites on the defective graphene-supported Cu19 clusters are all increased compared with those on the Cu19 clusters. The orbital-resolved, crystal orbital Hamilton population analysis demonstrates that the larger the integrated crystal orbital Hamilton population, the stronger the adsorption between the gas molecule and the bonded Cu atom. The center of antibonding states on the defective graphene-supported Cu19 is shifted upward relative to Fermi level compared to the corresponding one on pure Cu19 , which explains the enhanced adsorption energy on defective graphene-supported Cu19. In addition, the closer d-band center to the Fermi level on the defective graphene-supported Cu19 indicates a stronger adsorption capacity than on pure Cu19 .

Enhanced CO adsorption on α-graphyne-supported and defective graphene-supported Cu19 clusters and a modified induction energy model.

Ab initio molecular dynamics calculations were carried out to study the adsorption of CO on Cu19, α-graphyne-supported Cu19 and defective graphene-supported Cu19 clusters. The average adsorption energies on the three clusters are significantly increased by 68%, 104%, and 123% compared to the experimental value on the pristine Cu(110) surface. Furthermore, the α-graphyne-supported and defective graphene-supported Cu19 clusters exhibit greater adsorption strength than the pure Cu19 cluster, with 22% and 33% higher adsorption energies, respectively. The crystal orbital Hamilton population analysis shows that for the same type of adsorption site, the adsorption energy is linearly related to the bond interaction strength between the adsorbate and the substrate. We propose a modified induction energy model to predict the increase of chemisorption energy on α-graphyne-supported and defective graphene-supported Cu19 clusters based on the bare Cu19 cluster. The chemisorption energy enhancement predicted by the improved induction energy model has very good agreement with that calculated based on the ab initio molecular dynamics method and is more accurate than that predicted by the original induction energy model.

Ab Initio Molecular Dynamics Study of H2 Dissociation Mechanisms on Cu13 and Defective Graphene-supported Cu13 Clusters: Active Sites, Energy Barriers and Adsorption States.

Ab initio molecular dynamics calculations were performed to study H2 dissociation mechanisms on Cu13 and defective graphene-supported Cu13 clusters. The study reveals that seven types of corresponding dissociation processes are found on the two clusters. The average dissociation energy barriers are 0.51 eV on the Cu13 cluster and 0.12 eV on the defective graphene-supported Cu13 cluster, which are lowered by ~19 % and ~81 % compared with the pristine Cu(111) surface, respectively. Furthermore, compared with the pure Cu13 cluster, the average dissociation energy barrier on the defective graphene-supported Cu13 cluster is substantially reduced by about 76 %. The preferred dissociation mechanisms on the two clusters are H2 located at a top-bridge site with the barrier heights of 0.30 eV on the Cu13 cluster and -0.31 eV on the defective graphene-supported Cu13 cluster. Analysis of the H-Cu bond interactions in the transition states shows that the antibonding-orbital center shifts upward on the defective graphene-supported Cu13 cluster compared with the one on the Cu13 cluster, which explains the reduction of the dissociation energy barrier. The average adsorption energy of dissociated H atoms is also greatly enhanced on the defective graphene-supported Cu13 cluster, about twice that on the Cu13 cluster.

Atomic-Level Mechanism, Solvent Effect, and Potential of the Mean Force of the F- + CH3CH2Cl SN2 Reaction in Aqueous Solution.

We investigate the bimolecular nucleophilic substitution (SN2) reaction of F- with CH3CH2Cl in aqueous solution using combined multilevel quantum mechanism (ML-QM) theories with molecular mechanics (MM). The synchronized, atomic-level structural and charge evolutions are analyzed along the reaction path. The potential mean force along the reaction path in water is calculated at high-accuracy CCSD(T)/aug-cc-pVTZ/MM level of theory with a free energy barrier of 16.8 kcal/mol and a free energy of reaction of -9.7 kcal/mol. The water solvent hinders the reactivity by raising its reaction barrier by 15.1 kcal/mol, of which 13.6 kcal/mol comes from solvent energy contribution and 1.5 kcal/mol comes from the polarization effect. This indicates that the water solvent plays an essential role on this reaction in aqueous solution. We also predict the potential mean force profile based on the gas-phase reaction path and the solvation free energies of the stationary points; the comparison between our calculated result at CCSD(T)/MM level shows an excellent agreement with the predicted one with the free energy barrier at 16.2 kcal/mol and the free energy of reaction at -8.3 kcal/mol.

Theoretical dynamics studies of the CH3 + HBr → CH4 + Br reaction: integral cross sections, rate constants and microscopic mechanism.

Quantum and quasi-classical dynamics calculations have been performed for the reaction of HBr with CH3. The accurate ab initio-based potential energy surface function developed earlier for this reaction displays a potential well corresponding to a reactant complex and a submerged potential barrier. The integral cross sections were calculated on this potential energy surface using both a six-degree-of-freedom reduced dimensional quantum dynamics and the quasi-classical trajectory method and very good agreement was found between the two approaches. The cross sections were found to diverge when the collision energy decreases, indicating that the reactant attraction is responsible for the dynamics at low collision energy. The quantum mechanical and the quasi-classical rate constants also agree very well and almost exactly reproduce the experimental results at low temperatures up to 540 K. The negative activation energy observed experimentally is confirmed by the calculations and is a consequence of the long-range attraction between the reactants. From the classical trajectories mechanistic details have been extracted. It is found that at very low collision energy, the reacting system crosses the potential barrier because the forces within the complex guide them, although some 30% is reflected from the product side of the barrier. When the collision energy increases, the system does not follow the most favorable path and the reactants are, with increasing probability, reflected from the repulsive walls of the nonreactive parts of the reactants, providing a picture beyond the decreasing excitation function.

Predicting atomic-level reaction mechanisms for SN2 reactions via machine learning.

Identifying atomic-level reaction mechanisms is an essential step in chemistry. In this study, we develop a joint-voting model based on three parallel machine-learning algorithms to predict atomic-level and dynamical mechanisms trained with 1700 trajectories. Three predictive experiments are carried out with the training trajectories divided into ten, seven, and five classes. The results indicate that, as the number of trajectories in each class increases from the ten- to five-class model, the five-class model converges the fastest and the prediction success rate increases. The number of trajectories in each experiment to get the predictive models converged is 100, 100, and 70, respectively. The prediction accuracy increases from 88.3% for the ten-class experiment, to 91.0% for the seven-class, and to 92.0% for the five-class. Our study demonstrates that machine learning can also be used to predict elementary dynamical processes of structural evolution along time, that is, atomic-level reaction mechanisms.

Time-dependent quantum dynamics study of the F + C2H6 → HF + C2H5 reaction.

The reaction probabilities, integral cross sections, energy efficiency and rate constants are investigated for the F + C2H6 reaction using the quantum reaction dynamics, wave packet method. The ground-state integral cross section calculated using a six-degree-of-freedom approach is in very good agreement with the quasi-classical trajectory results. We find that the H-CH2CH3 stretching motion has the largest enhancement to reactivity, followed by the H-CH2-CH3 bending motion. However, the stretching motion between CH2 and CH3 slightly hinders the reactivity. The energy-form efficacy based on an equal amount of total energy shows that translational energy is more effective in enhancing the reactivity than vibrational energy of the H-CH2CH3 stretching motion at a relatively lower translational energy, while the reverse is true at a relatively high translational energy. An energy-shifting method is employed to calculate the full-dimensional rate constants. The quantum rate constants agree well with one of the two main experimental measurements, and the activation energy has an excellent agreement with the one calculated using canonical variational transition-state theory.

Theoretical investigation of the SN2 mechanism of X- [X = SH, PH2] + CH3Y [Y = F, Cl, Br, I] reactions in water.

We investigated the SN2 Walden-inversion mechanism of X- (X = SH, PH2) + CH3Y (Y = F, Cl, Br, I) reactions in water using multi-level quantum mechanics (ML-QM) and molecular mechanics (MM) methods. The potentials of the mean force were mapped using not only the density functional theory (DFT)/MM method but also a high-level, accurate CCSD(T)/MM method using the aug-cc-pVTZ basis set. In particular, for the PH2- + CH3I reaction, although the backside attack Walden-inversion mechanics were not observed in the gas phase, we found that this mechanism takes place in water. The atomic-level dynamics of the concerted SN2 mechanism and the stationary points along the reaction paths were characterized. For these reactions in water, their Walden-inversion barriers are higher than their corresponding ones in the gas phase, indicating that the aqueous solution hinders their reactivity. For the reactions with the same nucleophile X- in water, the reaction barrier heights with different leaving groups are in the order of F > Cl > Br > I. For the same leaving group Y with different nucleophiles SH- and PH2-, the reaction barrier with SH- is greater than that of PH2- due to the former having higher electronegativity than the latter.

Using quantum dynamics to study the effect of energy efficiency on the reactivity of the OH + DBr reaction.

We report a time-dependent, full dimensional, wave-packet calculation for the reaction of OH + DBr to examine the effect of the energy efficiency on the reactivity. This study shows that the vibrational excitations of the OH and DBr enhance the reaction. However, the rotational excitations of OH and DBr both hinder the reaction. As a result, the vibrational energies of both the OH and DBr reactants are more efficient at promoting the reactivity than the translational energy, while the rotational energies of OH and DBr are less effective than the translational energy. By analyzing the state population of the vibrational and rotational states along the reaction pathway, we also developed an approach in order to explain the enhancement of the vibrational excitation and the hindrance of the rotational excitation of the reaction. We found that the initial-state selected vibrational excited states of OH and DBr are the dominant components, respectively, for surmounting the barrier. However, the initial-state selected rotational excited states of OH and DBr are no longer the dominant states for surmounting the transition state owing to their population changes in the van der Waals well. This quantitative analysis demonstrates the potential well in the entrance valley plays an important role in the energy efficiency with regards to the reactivity.

Catalytic Descriptors to Investigate Catalytic Power in the Reaction of Haloalkane Dehalogenase Enzyme with 1,2-Dichloroethane.

Enzymes play a fundamental role in many biological processes. We present a theoretical approach to investigate the catalytic power of the haloalkane dehalogenase reaction with 1,2-dichloroethane. By removing the three main active-site residues one by one from haloalkane dehalogenase, we found two reactive descriptors: one descriptor is the distance difference between the breaking bond and the forming bond, and the other is the charge difference between the transition state and the reactant complex. Both descriptors scale linearly with the reactive barriers, with the three-residue case having the smallest barrier and the zero-residue case having the largest. The results demonstrate that, as the number of residues increases, the catalytic power increases. The predicted free energy barriers using the two descriptors of this reaction in water are 23.1 and 24.2 kcal/mol, both larger than the ones with any residues, indicating that the water solvent hinders the reactivity. Both predicted barrier heights agree well with the calculated one at 25.2 kcal/mol using a quantum mechanics and molecular dynamics approach, and also agree well with the experimental result at 26.0 kcal/mol. This study shows that reactive descriptors can also be used to describe and predict the catalytic performance for enzyme catalysis.

Oscillating collective motion of active rotors in confinement.

Due to its inherent out-of-equilibrium nature, active matter in confinement may exhibit collective behavior absent in unconfined systems. Extensive studies have indicated that hydrodynamic or steric interactions between active particles and boundary play an important role in the emergence of collective behavior. However, besides introducing external couplings at the single-particle level, the confinement also induces an inhomogeneous density distribution due to particle-position correlations, whose effect on collective behavior remains unclear. Here, we investigate this effect in a minimal chiral active matter composed of self-spinning rotors through simulation, experiment, and theory. We find that the density inhomogeneity leads to a position-dependent frictional stress that results from interrotor friction and couples the spin to the translation of the particles, which can then drive a striking spatially oscillating collective motion of the chiral active matter along the confinement boundary. Moreover, depending on the oscillation properties, the collective behavior has three different modes as the packing fraction varies. The structural origins of the transitions between the different modes are well identified by the percolation of solid-like regions or the occurrence of defect-induced particle rearrangement. Our results thus show that the confinement-induced inhomogeneity, dynamic structure, and compressibility have significant influences on collective behavior of active matter and should be properly taken into account.

The importance of the composite mechanisms with two transition states in the F- + NH2I SN2 reaction.

The dynamics of the bimolecular nucleophilic substitution (SN2) reactions at nitrogen are less understood than those of their corresponding reactions at carbon. In this paper, we report an ab initio molecular dynamics approach to investigate the reaction mechanisms of the F- + NH2I SN2 reaction at nitrogen. We found not only the one-transition-state mechanisms, but also the composite mechanisms with two and three transition states. For the two-transition-state mechanisms, the double inversion mechanism and the proton-abstraction roundabout followed by the backside-attack reaction mechanism have been reported before; but we discovered that there is also a new, front-side attack followed by the backside-attack Walden-inversion mechanism. Furthermore, a composite mechanism with three transition states also shows up in the reactive trajectories. Our results show that, as the collision energy increases, the SN2 reactivity decreases, and the proton-abstraction reactivity increases. The two-transition-state mechanisms, especially the double-inversion mechanism, make the largest contribution to the SN2 reactivity, followed then by the one-transition-state mechanisms, with the three-transition-state mechanism contributing the least. The potential energy profiles of the reaction mechanisms are characterized at the CCSD(T)/aug-cc-pVTZ(PP) level of theory. The analysis on stationary points shows that the proton-abstraction inversion transition state is ∼12.4 kcal mol-1 lower than the Walden-inversion transition state in contrast to the corresponding reaction at carbon F- + CH3I, in which the former is ∼26.1 kcal mol-1 higher than the latter. This might explain why the composite mechanism of the double inversion mechanism contributes the most to the SN2 reactivity in the F- + NH2I reaction.

Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy.

We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.

Multilevel Quantum Mechanics and Molecular Mechanics Study of the Double-Inversion Mechanism at Nitrogen: F- + NH2Cl in Aqueous Solution.

We employ a multilevel quantum mechanics and molecular mechanics method to investigate the double-inversion mechanism of the nucleophilic substitution reaction at the N center: the F- + NH2Cl reaction in aqueous solution. We find that the structures of the stationary points along the reaction path are quite different from the ones in the gas phase owing to the hydrogen-bond interactions between the solute and the surrounding water molecules. The atomic-level evolutions of the structures and charge transfer along the reaction path show that this double-inversion mechanism consists of an upside-down proton inversion process and a Walden-inversion process. The computed potential of mean force at the coupled-cluster singles and doubles with perturbative triples (CCSD(T))/molecular mechanics (MM) level of theory has the two-inversion barrier heights, and reaction free energy at 11.7, 29.6, and 12.6 kcal/mol, agreeing well with the predicted ones at 12.6, 32.5, and 12.2 kcal/mol obtained on the basis of the gas-phase reaction path and the solvation free energies of the stationary points.

Quantum dynamics study of kinetic isotope effects of OD with HBr and DBr.

We carried out a time-dependent, full dimensional, quantum dynamics wave-packet calculation to study the isotope effects for the OD + HBr and OD + DBr reactions. Reaction cross sections and rate constants for the OD + HBr (k2) and OD + DBr (k4) reactions are compared with the ones of OH + HBr (k1) and OH + DBr (k3). The comparisons of cross sections and rate constants show that OH/OD + HBr almost has the same reactivity, as does OH/OD + DBr. Nonetheless, the OH + HBr reaction still has the largest reactivity, then OD + HBr, OH + DBr, and OD + DBr has the smallest. Furthermore, the rate constants of OD + HBr/DBr reactions have a strong negative temperature dependence below 200 K and a nearly constant temperature dependence above 200 K, agreeing with the experimental results both qualitatively and quantitatively. Our calculated quantum primary kinetic isotope effects (k1/k3 = 1.56 and k2/k4 = 1.80) and secondary kinetic isotope effects (k1/k2 = 1.11 and k3/k4 = 1.29) are temperature independent, confirming the experimental measurements, and are in very good agreement with the experimental data.

Quantum dynamics calculations reveal temperature independence of kinetic isotope effect of the OH + HBr/DBr reaction.

The reaction of OH radicals with HBr plays a key role in atmospheric chemistry as the reaction, OH + HBr → Br + H2O, produces Br atoms that destroy ozone. The experimental measurements of the kinetic isotope effect of k(OH + HBr)/k(OH + DBr) found that the kinetic isotope effects are temperature-independent. However, previous quasi-classical trajectory calculations on an accurate ab initio potential energy surface showed that the kinetic isotope effect is temperature-dependent. By contrast, the present full-dimensional time-dependent quantum dynamics calculations on the same potential energy surface find that the kinetic isotope effect is temperature-independent, agreeing well with the experimental studies both qualitatively and quantitatively. Furthermore, the rate constants from both quantum dynamics and quasi-classical trajectory calculations have a peak at around 15 K whereas the experimental data are not available in this low temperature range. The good agreement of the temperature-dependence of kinetic isotope effects between the present quantum dynamics calculations and the experimental measurements indicates that the kinetic isotope effect of k(OH + HBr)/k(OH + DBr) should be temperature-independent and the peak of the rate constants from the theoretical calculations call for experimental measurements at a very low temperature range.

Newly proposed proton-abstraction roundabout with backside attack mechanism for the SN2 reaction at the nitrogen center in F- + NH2Cl.

Recent studies have improved our understanding of the mechanism and dynamics of the bimolecular nucleophilic substitution (SN2) reaction at the carbon center. Nonetheless, the SN2 reaction at the nitrogen center has received scarce attention and is less understood. Herein, we propose a new reaction mechanism for the SN2 reaction at the nitrogen center in the F- + NH2Cl reaction using ab initio molecular dynamics calculations. The newly proposed mechanism involves the rotation of NHCl with one proton of NH2Cl abstracted by the nucleophile, followed by the classical backside-attack process. The double-inversion mechanism revealed recently for the SN2 reaction at the carbon center is also observed for the title reaction at the nitrogen center. In contrast to the F- + CH3Cl reaction with a proton abstraction-induced first inversion transition state, the F- + NH2Cl reaction is a hydrogen bond-induced inversion. This newly proposed reaction mechanism opens a reaction channel to avoid the proton abstraction mechanism at low collision energy. The double-inversion mechanism of the title reaction with a negative first-inversion transition relative to the energy of the reactants is expected to have larger contribution to the reaction rate than the F- + CH3Cl reaction with a positive first-inversion transition state.

Catalytic Effect of Aqueous Solution in Water-Assisted Proton-Transfer Mechanism of 8-Hydroxy Guanine Radical.

Water-assisted proton-transfer process is a key step in guanine damage reaction by hydroxyl radical in aqueous solution. In this article, we quantitatively determine the solvent effect in water-assisted proton-transfer mechanism of 8-hydroxy guanine radical using combined quantum mechanics and molecular mechanism with an explicit solvation model. Atomic-level reaction pathway was mapped, which shows a synchronized two-proton-transfer mechanism between the assistant water molecule and 8-hydroxy guanine radical. The transition-state dipole moment is the largest along the reaction pathway, which electrostatically stabilizes the proton-transfer transition-state complex. The free-energy reaction barrier for this water-assisted proton-transfer reaction was calculated at 19.2 kcal/mol with the density functional theory/M08-SO/cc-pVTZ+/molecular mechanics level of theory. The solvent effect not only has a big impact on geometries, but also dramatically changes the energetics along the reaction pathway. Among the solvent effect contributions to the transition state, the solvent energy contribution is -28.5 kcal/mol and the polarization effect contribution is 19.9 kcal/mol. In total, the solvent effect contributes -8.6 kcal/mol to the free-energy barrier height, which means that the presence of aqueous solution has a catalytic effect on the reaction mechanism and enhances the proton-transfer reactivity in aqueous solution.

Multilevel Quantum Mechanics Theories and Molecular Mechanics Calculations of the Cl- + CH3I Reaction in Water.

The Cl- + CH3I → CH3Cl + I- reaction in water was studied using combined multilevel quantum mechanism theories and molecular mechanics with an explicit water solvent model. The study shows a significant influence of aqueous solution on the structures of the stationary points along the reaction pathway. A detailed, atomic-level evolution of the reaction mechanism shows a concerted one-bond-broken and one-bond-formed mechanism, as well as a synchronized charge-transfer process. The potentials of mean force calculated with the CCSD(T) and DFT treatments of the solute produce a free activation barrier at 24.5 and 19.0 kcal/mol, respectively, which agrees with the experimental one at 22.0 kcal/mol. The solvent effects have also been quantitatively analyzed: in total, the solvent effects raise the activation energy by 20.2 kcal/mol, which shows a significant impact on this reaction in water.

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution.

Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.