Potentials of Mean Force and Solvent Effects of the CN + CHX (X = F, Cl, Br, and I) Reactions by the N-Side Attack in Aqueous Solution.

A combined multilevel quantum mechanics and molecular mechanics approach is performed to investigate the nucleophilic substitution reactions of CN + CHX (X = F, Cl, Br, and I) by the N-side attack in aqueous solution. The water molecules are treated microscopically using an explicit SPC/E model, and the potentials of mean force are characterized by both the DFT and CCSD(T) levels of theory for the solute. Calculations demonstrate that the shielding effect of the solvent reduces the nucleophile-substrate and substrate-leaving group interactions in solution, leading to stationary point structures that are quite different from those in the gas phase.

Theoretical study of NH , H S, and HCN adsorption enhancement on defective graphene-supported Cu 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 NH , H S, and HCN on Cu and defective graphene-supported Cu 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.

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

molecular dynamics calculations were carried out to study the adsorption of CO on Cu, α-graphyne-supported Cu and defective graphene-supported Cu 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 Cu clusters exhibit greater adsorption strength than the pure Cu cluster, with 22% and 33% higher adsorption energies, respectively.

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

Ab initio molecular dynamics calculations were performed to study H dissociation mechanisms on Cu and defective graphene-supported Cu clusters. The study reveals that seven types of corresponding dissociation processes are found on the two clusters. The average dissociation energy barriers are 0.

Atomic-Level Mechanism, Solvent Effect, and Potential of the Mean Force of the F + CHCHCl S2 Reaction in Aqueous Solution.

We investigate the bimolecular nucleophilic substitution (S2) reaction of F with CHCHCl 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.

Theoretical dynamics studies of the CH + HBr → CH + 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 CH. The accurate -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.

Predicting atomic-level reaction mechanisms for S2 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.

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

The reaction probabilities, integral cross sections, energy efficiency and rate constants are investigated for the F + CH 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-CHCH stretching motion has the largest enhancement to reactivity, followed by the H-CH-CH bending motion.

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.

Theoretical investigation of the S2 mechanism of X [X = SH, PH] + CHY [Y = F, Cl, Br, I] reactions in water.

We investigated the S2 Walden-inversion mechanism of X (X = SH, PH) + CHY (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 PH + CHI reaction, although the backside attack Walden-inversion mechanics were not observed in the gas phase, we found that this mechanism takes place in water.

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.

The importance of the composite mechanisms with two transition states in the F + NHI S2 reaction.

The dynamics of the bimolecular nucleophilic substitution (S2) 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 + NHI S2 reaction at nitrogen. We found not only the one-transition-state mechanisms, but also the composite mechanisms with two and three transition states.

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.

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.

Multilevel Quantum Mechanics and Molecular Mechanics Study of the Double-Inversion Mechanism at Nitrogen: + 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 center: the + 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.

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.

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 + HO, 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.

Newly proposed proton-abstraction roundabout with backside attack mechanism for the S2 reaction at the nitrogen center in F + NHCl.

Recent studies have improved our understanding of the mechanism and dynamics of the bimolecular nucleophilic substitution (S2) reaction at the carbon center. Nonetheless, the S2 reaction at the nitrogen center has received scarce attention and is less understood. Herein, we propose a new reaction mechanism for the S2 reaction at the nitrogen center in the F + NHCl reaction using ab initio molecular dynamics calculations.

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.

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

The Cl + CHI → CHCl + 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.

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.

Multi-level quantum mechanics theories and molecular mechanics study of the double-inversion mechanism of the F + CHI reaction in aqueous solution.

A double-inversion mechanism of the F + CHI reaction was discovered in aqueous solution using combined multi-level quantum mechanics theories and molecular mechanics. The stationary points along the reaction path show very different structures to the ones in the gas phase due to the interactions between the solvent and solute, especially strong hydrogen bonds. An intermediate complex, a minimum on the potential of mean force, was found to serve as a connecting-link between the abstraction-induced inversion transition state and the Walden-inversion transition state.

Quantum Dynamics Study of the Potential Energy Minima Effect on Energy Efficiency for the F + CHCl → FCH + Cl Reaction.

The Polanyi rules on the energy efficiency on reactivity are summarized solely from the locations of barriers on the potential energy surfaces. Here, our quantum dynamics study for the F + CHCl → FCH + Cl reaction shows that the two potential energy minima in the entrance channel on the potential energy surface play an essential role in energy efficiency on reactivity. The reactivity of this reaction is dominated by the low collision energies where two distinctive reaction mechanisms involve the two minima in the entrance channel.

Quantum dynamics study of energy requirement on reactivity for the HBr + OH reaction with a negative-energy barrier.

A time-dependent, quantum reaction dynamics approach in full dimensional, six degrees of freedom was carried out to study the energy requirement on reactivity for the HBr + OH reaction with an early, negative energy barrier. The calculation shows both the HBr and OH vibrational excitations enhance the reactivity. However, even this reaction has a negative energy barrier, the calculation shows not all forms of energy are equally effective in promoting the reactivity.

A new, double-inversion mechanism of the F + CHCl S2 reaction in aqueous solution.

Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F + CHCl S2 reaction in the gas phase [Nat. Commun.