Intrinsic Reaction Coordinate Research Articles

Dynamical Bifurcation in Gas-Phase XH- + CH3 Y SN 2 Reactions: The Role of Energy Flow and Redistribution in Avoiding the Minimum Energy Path.

The gas-phase reactions of XH- (X=O, S) + CH3 Y (Y=F, Cl, Br) span nearly the whole range of SN 2 pathways, and show an intrinsic reaction coordinate (IRC) (minimum energy path) with a deep well owing to the CH3 XH⋅⋅⋅Y- (or CH3 S- ⋅⋅⋅HF) hydrogen-bonded postreaction complex. MP2 quasiclassical-type direct dynamics starting at the [HX⋅⋅⋅CH3 ⋅⋅⋅Y]- transition-state (TS) structure reveal distinct mechanistic behaviors. Trajectories that yield the separated CH3 XH+Y- (or CH3 S- +HF) products directly are non-IRC, whereas those that sample the CH3 XH⋅⋅⋅Y- (or CH3 S- ⋅⋅⋅HF) complex are IRC. The IRCIRC/non-IRC ratios of 90:10, 40:60, 25:75, 2:98, 0:100, and 0:100 are obtained for (X, Y)=(S, F), (O, F), (S, Cl), (S, Br), (O, Cl), and (O, Br), respectively. The properties of the energy profiles after the TS cannot provide a rationalization of these results. Analysis of the energy flow in dynamics shows that the trajectories cross a dynamical bifurcation, and that the inability to follow the minimum energy path arises from long vibration periods of the X-C⋅⋅⋅Y bending mode. The partition of the available energy to the products into vibrational, rotational, and translational energies reveals that if the vibrational contribution is more than 80 %, non-IRC behavior dominates, unless the relative fraction of the rotational and translational components is similar, in which case a richer dynamical mechanism is shown, with an IRC/non-IRC ratio that correlates to this relative fraction.

On the Driving Force of the Excited-State Proton Shuttle in the Green Fluorescent Protein: A Time-Dependent Density Functional Theory (TD-DFT) Study of the Intrinsic Reaction Path.

We simulated the intrinsic reaction path of the Green Fluorescent Protein (GFP) proton shuttle in both the ground state (S0) and first singlet excited state (S1), accounting for the main energetic and steric effects of the protein in a convenient model including the chromophore, the crystallographic water, and the residues directly involved in the proton transfer event. We adopted density functional theory (DFT) and time-dependent density functional theory (TD-DFT) levels to define the potential energy surfaces of the two electronic states, and we compared results obtained by the Damped Velocity Verlet and the Hessian-based Predictor-Corrector integrators of the intrinsic reaction coordinate, which gave a comparable and consistent picture of the mechanism. We show that, at S1, the GFP proton transfer becomes favored, with respect to S0, as suggested by the experimental evidence. As an important finding, this change is strictly related to the rearrangement of the hydrogen bond network composing the reaction path, which, in S1, relaxes to a tighter and planar configuration, as a consequence of the photoinduced relaxation in the GFP chromophore structure, thus prompting more effectively for the proton shuttle. Therefore, we give an unprecedented direct proof of the key role played by the photoinduced structural relaxation of the GFP on the chromophore photoacidity, validating, in particular, the hypothesis of Fang and co-workers [Nature 2009, 462, 200].

Extraction of H2 from H2O molecule using a small Al6Si cluster

A three-step reaction for the complete extraction of H2 from H2O molecule using a small Al6Si cluster is determined based on first-principle calculations. All reactants, products, and transition states are found through optimization calculation and confirmed frequency analysis. The intrinsic reaction coordinate is also calculated to validate the reaction process. Charge distribution is used to analyze the novel reaction. The present results show that the entire reaction can be actively started when the H2O molecule is adsorbed on Al6Si cluster because the barrier of the first transition state only 0.1448 eV and the whole process is an exothermic reaction when zero-point energy is included. It is found that Al6Si cluster can strongly capture H2O molecule, as well as extract and store the H2 molecule, at a favorable temperature. This result may serve as a basis for the development of a more efficient method of generating and storing H2 from H2O molecule.

Diazomethane addition to sumanene as a subfullerene structure: A theoretical mechanistic study

In present study, kinetics and reaction mechanism of diazomethane and sumanene in gas phase were studied using quantum calculations at B3LYP/6-311+G(d,p) level of theory. Functionalization of the sumanene by this reaction was investigated in proposed fourteen pathways for different kinds of CC bond. Vibrational frequencies analysis and intrinsic reaction coordinate (IRC) calculations were carried out and the rate constants for all paths were calculated by using canonical transition state theory (CTST). The best and the worst paths and dominant products for this reaction were determined. Stability of the intermediates, transition sates and products was discussed. Results showed that in the first step of CH2N2 addition to sumanene and formation of corresponding transition state, hub position has the least and rim position has the most barrier energy. Also, for all types of CC bond, sumanene with a CH2 group as a bridge was formed and conversion of a sumanene hexagon to heptagon happened for all positions except spoke. Generally, diazomethane can add a CH2 group in the carbon chain, insert CH2 group as a bridge or add a CH3 group to the structure.

An Integrated Experimental and Computational Approach for Characterizing the Kinetics and Mechanism of TriadimefonRacemization.

Enantiomers of chiral molecules commonly exhibit differing pharmacokinetics and toxicities, which can introduce significant uncertainty when evaluating biological and environmental fates and potential risks to humans and the environment. However, racemization (the irreversible transformation of one enantiomer into the racemic mixture) and enantiomerization (the reversible conversion of one enantiomer into the other) are poorly understood. To better understand these processes, we investigated the chiral fungicide, triadimefon, which undergoes racemization in soils, water, and organic solvents. Nuclear magnetic resonance (NMR) and gas chromatography / mass spectrometry (GC/MS) techniques were used to measure the rates of enantiomerization and racemization, deuterium isotope effects, and activation energies for triadimefon in H2 O and D2 O. From these results we were able to determine that: 1) the alpha-carbonyl carbon of triadimefon is the reaction site; 2) cleavage of the C-H (C-D) bond is the rate-determining step; 3) the reaction is base-catalyzed; and 4) the reaction likely involves a symmetrical intermediate. The B3LYP/6-311+G** level of theory was used to compute optimized geometries, harmonic vibrational frequencies, nature population analysis, and intrinsic reaction coordinates for triadimefon in water and three racemization pathways were hypothesized. This work provides an initial step in developing predictive, structure-based models that are needed to identify compounds of concern that may undergo racemization. Chirality 28:633-641, 2016. © 2016 Wiley Periodicals, Inc.

Orbital Energy-Based Reaction Analysis of SN2 Reactions

An orbital energy-based reaction analysis theory is presented as an extension of the orbital-based conceptual density functional theory. In the orbital energy-based theory, the orbitals contributing to reactions are interpreted to be valence orbitals giving the largest orbital energy variation from reactants to products. Reactions are taken to be electron transfer-driven when they provide small variations for the gaps between the contributing occupied and unoccupied orbital energies on the intrinsic reaction coordinates in the initial processes. The orbital energy-based theory is then applied to the calculations of several S N2 reactions. Using a reaction path search method, the Cl− + CH3I → ClCH3 + I− reaction, for which another reaction path called “roundabout path” is proposed, is found to have a precursor process similar to the roundabout path just before this SN2 reaction process. The orbital energy-based theory indicates that this precursor process is obviously driven by structural change, while the successor SN2 reaction proceeds through electron transfer between the contributing orbitals. Comparing the calculated results of the SN2 reactions in gas phase and in aqueous solution shows that the contributing orbitals significantly depend on solvent effects and these orbitals can be correctly determined by this theory.

Spherical conformational landscape shed new lights on fluxional nature of cyclopentane and its derivatives, confirmed by their Raman spectra

A detailed conformational analysis of cyclopentane and its derivatives were performed using DFT ωb97xd/6-311+G(d,p) level of theory. Intrinsic Reaction Coordinate (IRC) computations augmented with frequency computations were used to figure out a way to assemble four pseudorotational platforms into a final hyper-surface which can elaborately describe the vibrational pattern in Raman spectra of five membered ring compounds. The spherical conformational landscape represents two concentric ring coordinates for twisting and bending pathways in cyclopentane and its derivatives. The two ring coordinates work hand-in-hand to support the very intrinsic property of this molecule, its fluxional nature, coded intricately into the D/G band region (1100–1600cm−1) of its Raman spectrum. This fluxional nature seems to cope with almost any rigidity imposed by either temperature or structural restrictions. The same rationale was also used to resolve a hyper-surface for the fused five membered rings, octahydropentalenes. Further investigations are needed to shed light on the so called sugar pucker conformational wheels in DNA, B and A helices.

The non-IRC mechanism of OH anion reaction with CH3OOH revealed by direct dynamics simulations

Organic peroxides are temporary reservoirs for oxidizing radicals and are involved in the formation of acid rain, so it is important to remove them in the atmosphere. The elimination reaction of CH3OOH with hydroxide anion has been investigated by direct dynamics simulations at PBE0/6-311+G(d,p) level of theory. Two products channels, CH3OO−+H2O and H2O+CH2O+HO−, are observed. 44% formed CH3OO−+H2O, the major product reaction channel observed in experiment, 27% formed HO−+CH2O+H2O and remaining 29% trajectories went back to the reactants. The simulations reveal that two reaction channels occur by both direct and indirect events and dominate by the direct mechanism. The non-IRC behavior is found for this reaction, that the much higher energy non-IRC products CH3OO−+H2O and H2O+CH2O+HO− were formed, instead of the more exothermic products H2O+CH2(OH)O− as predicted by the intrinsic reaction coordinate (IRC).

Theoretical and experimental studies on proton transfer in acetate-based protic ionic liquids

In this study, the proton transfer of three protic ionic liquids (PILs) pyrrolidinium acetate ([Pyrrol]OAc), diethylammonium acetate ([DEA]OAc) and bis-(2-methoxyethyl)-ammonium acetate ([BMOEA]OAc) were investigated. At first, the structures of the ion-pairs and molecular pairs of these PILs were optimized at B3LYP/6-311++G(d,p) level. The interaction energy between anions and cations was also obtained. The proton transfer processes were verified by intrinsic reaction coordinate (IRC) pathways tracing to the energy profiles connecting the transition state (TS) to the two desired minima, i.e. ion pair and molecular pair. The experimental attenuated total reflection (ATR) FTIR spectra of these PILs at room temperature were determined and compared with the results calculated at B3LYP/6-311++G(d,p) level. Vibrational mode analyses (VMA) for [Pyrrol]OAc found that δ(NH) has an imaginary frequency (−147.3cm−1), which is accounted for proton transfer from [NH2]+ to OAc−. Natural bond orbital (NBO) analyses pointed out that second order perturbation stabilization energy of (E(2)) of LP(N1)→σ*(O2-H5) was much larger than that of other orbitals, and should be the symmetrical matching with the maximum overlap and the minimum gap (0.73au). The hybridized index of N atom is varied from sp3.65 in ionic pair to sp4.49 in TS. The constituent of s orbital decreases 3.3% and the length of N1-H5 increases from 1.02Å in ionic pair to 1.65Å in TS, and the symmetric stretching vibration takes place the red shift. It could be explained that the N1-O2-H5 played an important role in the stabilization of molecular pair. The electron density ρ(r) and the Laplacian of the electron density ∇2ρ(r) derived from atoms in molecules (AIM) analyses were used to describe the intensity and characteristic of a bond. The results indicate that a very strong interaction of the hydrogen bonds exists in the ion-pair geometries and the bonds are the covalent bond.

Generating H2 from a H2O molecule by catalysis using a small Al6Cu cluster

Only one H atom is extracted from a single H2O molecule in a usual reaction for hydrogen generation. In this study, a three-step reaction has been identified for completely extracting H2 from H2O molecule with the catalysis of a small Al6Cu cluster, based on the first principles calculations. All the reactants, products, and transition states are determined by optimization calculation and confirmed by frequency analysis. The intrinsic reaction coordinate is also calculated to validate the reaction process. Results show that the whole reaction is an endothermic reaction. The charge distribution is used to understand the novel reaction. It is found that Al6Cu cluster can strongly capture H2O molecule and extract the H2 molecule completely, which may present a more efficient way to generate H2 from a single H2O molecule.

Functionalization of the sumanene by nitrous oxide: A mechanistic study

The mechanistic study of the cycloaddition reaction of nitrous oxide onto sumanene nanostructure carried out systematically using quantum chemistry methods. The 1,3-dipolar cycloaddition reaction of nitrous oxide with different kinds of C–C bond of sumanene in thirteen pathways was investigated. Geometry of reactants, transition states, intermediates and products were optimized at B3LYP/6-311+G(d) level of theory. Vibrational frequencies and relative energies for all stationary points were determined. Thirty-three transition states were identified for all pathways and confirmed by intrinsic reaction coordinate (IRC) calculations. The rate constants for all paths were calculated by using canonical transition state theory (CTST). Results showed that N2O addition to flank position is more favorable than other positions of sumanene, energetically. The major products are sumanene with an epoxide group in flank, spoke and hub6 positions; also products with an enol or oxepin group in rim and hub5 positions, respectively. Also, for all five positions, in the first step, C21H12N2O with a pentagon heterocycle contain O–N–N will be formed. In subsequent steps, either N2 extrusion or rearrangement can be done. Products related to outer positions of sumanene are more stable than corresponding products related to middle positions of sumanene (hub and spoke).

Computational and mechanistic studies of the acylation of cyclopropanes

As the well known protonated cyclopropanes’ present calculations confirm the existence of acetylated cyclopropanes, we describe the structure of edge- and corner-acetylated cyclopropanes rising from the energetically favored addition of acetyl cation to cyclopropanes. Some of those explain the few available experimental results concerning the acetylation reaction of cyclopropanes. Structures have been calculated at the B3LYP/6-311++G(3df,3pd) and MP2/6-311++G(3df,3pd) levels of theory in ideal gas and in dichloromethane as solvent. Transition state geometries in ideal gas and in dichloromethane as solvent were confirmed by intrinsic reaction coordinate (IRC) calculations.

DFT STUDY ON HYDROGENATION REACTION OF ACETALDEHYDE TO ETHANOL IN GAS AND WATER PHASE

Numerical investigation of hydrogenation reaction of acetaldehyde to ethyl alcohol has been done in two phases, i.e. gaseous and aqueous phase separately using Gaussian 09 software package. For aqueous phase calculations, solvation approach has been taken and applied SMD model with water as solvent. Geometries were optimized at B3LYP functional of density functional theory (DFT) with the basis set of 6-31g(d) in both the phases. An imaginary frequency in frequency calculation result affirms the transition state. For getting an optimized structures of reactant and product, intrinsic reaction coordinate (IRC) calculation is carried out on the transition state structure at the same level of theory, in both phases. IRC connects the both minima in both forward and backward directions linking with transition state structure. Single point energy (SPE) has been calculated to get more accurate values of the optimized structures of reactant, product and transition state in both phases, i.e., gas and water at CCSD/6-311+g(3df,2p) theory.

ChemInform Abstract: Intrinsic Reaction Coordinate: Calculation, Bifurcation, and Automated Search

AbstractReview: 173 refs.

Theoretical study of two states reactivity of NO activation on iron atom

The mechanism of Fe+NO was calculated by the Density Functional Theory (DFT) with the B3LYP methods combined with the 6-311+G (d, p) basis set. The geometry of reactants, transition states, intermediates and products of two reaction systems were completely optimized, and all the transition states were verified by the vibration analysis and intrinsic reaction coordinate (IRC) calculations. The “Two State Reactivity (TSR)” was used to analyze the reaction mechanisms; Results showed that the reaction system preferentially involves low-spin state entrance channel and the high-spin state exit channel. In the reaction channel, the crossing point appears, which would effectively reduce the activation energy and increase the release of reaction heat, play a significant and beneficial role in the kinetic and thermodynamic aspects of this catalytic reaction.

Kinetics investigation of the hydrogen abstraction reaction between CH3SS and CN radicals.

The reaction mechanisms and rates for the H abstraction reactions between CH3SS and CN radicals in the gas phase were investigated with density functional theory (DFT) methods. The geometries, harmonic vibrational frequencies, and energies of all stationary points were obtained at B3PW91/6-311G(d,p) level of theory. Relationships between the reactants, intermediates, transition states and products were confirmed, with the frequency and the intrinsic reaction coordinate (IRC) analysis at the same theoretical level. High accurate energy information was provided by the G3(MP2) method combined with the standard statistical thermodynamics. Gibbs free energies at 298.15 K for all of the reaction steps were reported, and were used to describe the profile diagrams of the potential energy surface. The rate constants were evaluated with both the classical transition state theory and the canonical variational transition state theory, in which the small-curvature tunneling correction was included. A total number of 9 intermediates (IMs) and 17 transition states (TSs) were obtained. It is shown that IM1 is the most stable intermediate by the largest energy release, and the channel of CH3SS + CN → IM3 → TS10 → P1(CH2SS + HCN) is the dominant reaction with the lowest energy barrier of 144.7 kJ mol(-1). The fitted Arrhenius expressions of the calculated CVT/SCT rate constants for the rate-determining step of the favorable channel is k =7.73 × 10(6) T (1.40)exp(-14,423.8/T) s(-1) in the temperature range of 200-2000 K. The apparent activation energy E a(app.) for the main channel is -102.5 kJ mol(-1), which is comparable with the G3(MP2) energy barrier of -91.8 kJ mol(-1) of TS10 (relative to the reactants).

Multiple approach to model unpaired spin density effects in H-ZSM5 zeolite with extra-framework O atom: H-abstraction reaction from methane

The interaction of methane with an extra-framework oxygen atom in acidic zeolite (H-ZSM5) porous substrate has been investigated by means of different state of the art calculations using two model systems in their triplet spin state: zeolite was modelled both by its crystallographic structure subject to periodic boundary condition and by cluster approach in gas-phase. We have evaluated the energetics of H-abstraction reaction from methane within the (010) straight channel of acidic zeolite by different computational approaches. First by in bulk plane waves Density Functional Theory (with and without dispersion energy correction) and then, in gas-phase cluster, by typical quantum chemistry approaches based on molecular orbital theory, where electronic wave function is expanded in Gaussian basis sets, within variational or perturbative schemes. Reaction paths have been determined either by Climbing Image Nudged Elastic Band method (c-NEB) in bulk or by Intrinsic Reaction Coordinate (IRC) method in gas phase. Transition State has been characterized in cluster models using Becke-3-Lee Yang Parr (B3LYP) and BeckeHalf&HalfLeeYangParr (BHLYP) hybrid functionals. Calculated energy barriers and all results allow an interesting vis-à-vis of commonly used, alternative, often exclusive models. This study indicates that open shell systems composed of O atoms and H-ZSM5 are worth to be considered in H-abstraction from small hydrocarbons in applicative processes.

Hydrogen storage in small size MgnCo clusters: A density functional study

The present study reports the use MgnCo (n = 1–10) hybrid nanoclusters as hydrogen storage using density functional theory (DFT) calculation method. From the variation of the thermodynamic parameters of the clusters Mg4Co and Mg6Co are found stable in the series, whereas, after absorption of hydrogen, the higher stability shifted to H2-Mg5Co. It is found that after reaction with the cluster, hydrogen atoms adsorbed with Co atom in MgnCo clusters to form MgnCoH2 that gives a better option in hydrogen catalysis. By the calculated values of chemisorptions and physisorptions energies; VIP and VEA parameters, we found Mg5Co can be used as effective hydrogen catalysis. Calculated chemisorptions energy of the H2-Mg5Co cluster is found maximum in the series. The calculated activation barrier energy of H2-Mg5Co has been verified by the study of intrinsic reaction coordinates (IRC) pathway between Mg5Co and H2.

Computational study of the gas phase reaction of hydrogen azide and corannulene: A DFT study

The present computational study aims to better understand the nature of the gas phase reaction mechanism of corannulene and hydrogen azide molecules using MP2/6-311+G(d,p)//B3LYP/6-31+G(d) level of theory. The reactions of hydrogen azide with various kinds of C–C bond of corannulene in eleven pathways were considered. Vibrational analysis and intrinsic reaction coordinate (IRC) calculations were done and the rate constants for all paths were calculated by using canonical transition state theory (CTST). Results showed that rim position and after that hub position are the best for functionalization of corannulene with hydrazoic acid molecule, energetically and the major products are corannulene with an aziridine group in rim and hub positions, respectively. Addition of HN3 to flank and spoke positions of corannulene and 1,4-addition of HN3 are endothermic in all investigated pathways. For flank position, only a triazoline intermediate is produced and elimination of N2 or other pathways does not proceed.

Geometry, vibrational frequency, and isomerization of neutral and cation Cu–CN complex

The geometry structure, vibrational frequency, and the isomerization of neutral and cation copper cyanide systems ( CuCN and CuCN +) were investigated by employing three DFT methods (B3LYP, B3P86 and B3PW91) and MP2 functional with 6-311+G* basis set. The cyanides CuCN (1Σ+) is the most stable one among the isomers of CuCN , and CuNC +(2Σ+) isocyanides is the global minimum on its potential energy surface (PES). The vibrational modes of these isomers were assigned. Two dissociation mechanisms were designed for each species. The complex ( CuCN and CuCN +) tends to dissociate through neutral mechanism into CN cluster. The useful information is brought forward about the synthesis of material and biological macromolecule. The state–state isomerization pathways were established using the intrinsic reaction coordinate (IRC).