Potential Energy Surface For Reaction Research Articles

Study of the potential energy surface of reactions in a system containing <i>i</i>-propyl and <i>n</i>-propyl radicals

The energy pathways of possible decomposition and isomerization reactions of iso-propyl (i-C3H7) and n-propyl (n-C3H7) radicals have been studied by computational methods of quantum chemistry. B3LYP, M062X, MP2, and CBS-QB3 methods are used to localize stationary points on the potential energy surface of a system containing propyl radicals. A number of intermediate compounds formed during the isomerization and decomposition of propyl radicals have been identified, and information has been obtained on their structure and thermochemical parameters. Based on the results of the research, a diagram of the energy levels of the system under consideration was constructed.

Low temperature dynamics of H + HeH+→ H2+ + He reaction: On the importance of long-range interaction.

While the growing realization of the importance of long-range interactions is being demonstrated in cold and ultracold bimolecular collision experiments, their influence on one of the most critical ion-neutral reactions has been overlooked. Here, we address the non-Langevin abrupt decrease observed earlier in the low-energy integral cross-sections and rate coefficients of the astrochemically important H + HeH+→ H2+ + He reaction. We attribute this to the presence of artificial barriers on existing potential energy surfaces (PESs). By incorporating precise long-range interaction terms, we introduce a new refined barrierless PES for the electronic ground state of HeH2+ reactive system, aligning closely with high-level abinitio electronic energies. Our findings, supported by various classical, quantum, and statistical methods, underscore the significance of long-range terms in accurately modeling reactive PESs. The low-temperature rate coefficient on this new PES shows a substantial enhancement as compared to the previous results and aligns with the Langevin behavior. This enhancement could noticeably affect the prediction of HeH+ abundance in early Universe condition.

Nitrosation mechanisms, kinetics, and dynamics of the guanine and 9-methylguanine radical cations by nitric oxide-Radical-radical combination at different electron configurations.

As a precursor to various reactive nitrogen species formed in biological systems, nitric oxide (•NO) participates in numerous processes, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. Forming guanine radical cations is another common DNA lesion resulting from ionization and oxidation damage. As such, the interaction of •NO with guanine radical cations (G•+) may contribute to the radiosensitization of •NO. An intriguing aspect of this process is the participation of multiple spin configurations in the reaction, including open-shell singlet 1,OS[G•+(↑)⋯(↓)•NO], closed-shell singlet 1,CS[G(↑↓)⋯NO+], and triplet 3[G•+(↑)⋯(↑)•NO]. In this study, the reactions of •NO with both unsubstituted guanine radical cations (in the 9HG•+ conformation) and 9-methylguanine radical cations (9MG•+, a guanosine-mimicking model compound) were investigated in the absence and presence of monohydration of radical cations. Kinetic-energy dependent reaction product ions and cross sections were measured using an electrospray ionization guided-ion beam tandem mass spectrometer. The reaction mechanisms, kinetics, and dynamics were comprehended by interpreting the reaction potential energy surface using spin-projected density functional theory, coupled cluster theory, and multiconfiguration complete active space second-order perturbation theory, followed by RRKM kinetics modeling. The combined experimental and computational findings revealed closed-shell singlet 1,CS[7-NO-9MG]+ as the major, exothermic product and triplet 3[8-NO-9MG]+ as the minor, endothermic product. Singlet biradical products were not detected due to high reaction endothermicities, activation barriers, and inherent instability.

Revisiting a Chemical Route to the Formation of CN− in the Interstellar Medium

We discuss the HCN + H− reaction as a path to the formation of CN−, the smallest cyanopolyyne anion observed in several interstellar environments. We first obtain the new ab initio reactive potential energy surface using a full 5D representation, where only the C–N bond is kept fixed, and discuss the neural network procedure employed to yield an accurate fit for the dynamics. The reaction is then investigated by using a quasi-classical trajectory approach to scan the low-temperature range of the dark molecular clouds where the anion has been sighted. Calculations are extended to room temperature to make a successful comparison with existing experimental data. We further present reduced dimensionality modeling of the reaction as a 2D process within a variational-transition state treatment with the inclusion of long-range forces. The dominant role of such forces in producing large reaction rate coefficients is discussed for both treatments, which yield very similar sizes and behavior of such coefficients from 50 to 300 K. The implications of our results for the interstellar medium formation of the CN− species via this chemical route are discussed, suggesting its greater significance over the radiative electron attachment paths, whose rate coefficients were found by recent calculations to be orders of magnitude smaller.

Theoretical study of the mechanism of 2F-molecular sieve domain chiral transition of Asn molecules

Abstract Using density functional theory at the level of oniom (b3lyp/6-31g (d, p): uff), we investigated the chiral transition process of the Asparagine molecule in 2F-MOL. Furthermore, a complete chiral transition path reaction potential energy surface was drawn by looking for the extreme value point structures including the transition state and intermediate. The results show that the hydrogen atom on the chiral carbon atom of S-Asparagine molecule can transfer to the other side of the carbon atom via the oxygen atoms of carboxyl atoms as a bridge, to achieve the chiral transition of Asparagine molecule from S-type to R-type. On this path there is four intermediate and five transition states. The biggest reaction energy barrier is 243.9089KJ/mol derived from the fourth transition state TS1-R-Asn@2F-MOL.

Unveiling the Reaction Mechanism of the N(2D) + Pyridine Reaction: Ring-Contraction versus 7-Membered-Ring Formation Channels.

Despite the relevance of the reactions of the prototypical nitrogen-containing six-membered aromatic molecule (N-heterocyclic) of pyridine (C6H5N) in environmental science, astrochemistry, planetary science, prebiotic chemistry, and materials science, few experimental/theoretical studies exist on the bimolecular reactions involving pyridine and neutral atomic/molecular radicals. We report a combined experimental and theoretical study on the elementary reaction of pyridine with excited nitrogen atoms, N(2D), aimed at providing information about the primary reaction products and their branching fractions (BFs). From previous crossed molecular beam (CMB) experiments with mass-spectrometric detection and present synergistic calculations of the reactive potential energy surface (PES) and product BFs we have unveiled the reaction mechanism. It is found that the reaction proceeds via N(2D) barrierless addition to pyridine that, via bridged intermediates followed by N atom "sliding" into the ring, leads to 7-membered-ring structures. They further evolve, mainly via ring-contraction mechanisms toward 5-membered-ring radical products and, to a smaller extent, via H-displacement mechanisms toward 7-membered-ring isomeric products and their isomers. Using the theoretical statistical estimates, an improved fit of the experimental data previously reported has been obtained, leading to the following results for the dominant product channels: C4H4N (pyrrolyl) + HCN (BF = 0.61 ± 0.20), C3H3N2 (1H-imidazolyl/1H-pyrazolyl) + C2H2 (BF = 0.11 ± 0.06), and C5H4N2 (7-membered-ring molecules or pyrrole carbonitriles) + H (BF = 0.28 ± 0.10). The ring-contraction product channels C4H4N (pyrrolyl) + HCN, C3H3N2 (1H-imidazolyl) + C2H2, C3H3N2 (1H-pyrazolyl) + C2H2, and C5H5 (cyclopentadienyl) + N2 have statistical BFs of 0.54, 0.09, 0.11, and 0.07, respectively. Among the H-displacement channels, the cyclic-CHCHCHCHNCN + H channel and cyclic-CHCHCHCHCN2 + H are theoretically predicted to have a comparable BF (0.07 and 0.06, respectively), while the other isomeric 7-membered-ring molecule + H channel has a BF of 0.03. Pyrrole-carbonitriles and 1H-ethynyl-1H-imidazole (+ H) isomeric channels have an overall BF of 0.03. Implications for the chemistry of Saturn's moon Titan and prebiotic chemistry, as well as for understanding the N-doping of graphene or carbon nanotubes, are noted.

Multi-Level Protocol for Mechanistic Reaction Studies Using Semi-Local Fitted Potential Energy Surfaces.

In this work, we propose a multi-level protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged Elastic Band (NEB) method driven by a cheap electronic structure method. Forces recalculated at the more accurate electronic structure theory for a set of points on the path are fitted with a machine learning technique (in our case symmetric gradient domain machine learning or sGDML) to produce a semi-local reactive potential energy surface (PES), embracing reactants, products and transition state (TS) regions. This approach has been successfully applied to a unimolecular (Bergman cyclization of enediyne) and a bimolecular (SN2 substitution) reaction. In particular, we demonstrate that with only 50 to 150 energy-force evaluations with the accurate reference methods (here complete-active-space self-consistent field, CASSCF, and coupled-cluster singles and doubles, CCSD) it is possible to construct a semi-local PES giving qualitative agreement for stationary-point geometries, intrinsic reaction coordinates and barriers. Furthermore, we find a qualitative agreement in vibrational frequencies and reaction rate coefficients. The key aspect of the method's performance is its multi-level nature, which not only saves computational effort but also allows extracting meaningful information along the reaction path, characterized by zero gradients in all but one direction. Agnostic to the nature of the TS and computationally economic, the protocol can be readily automated and routinely used for mechanistic reaction studies.

Merged-Beams Study of the Reaction of Cold HD+ with C atoms Reveals a Pronounced Intramolecular Kinetic Isotope Effect

We present a merged-beams study of reactions between HD+ ions, stored in the Cryogenic Storage Ring (CSR), and laser-produced ground-term C atoms. The molecular ions are stored for up to 20 s in the extreme vacuum of the CSR, where they have time to relax radiatively until they reach their vibrational ground state (within 0.5 s of storage) and rotational states with J≤3 (after 5 s). We combine our experimental studies with quasiclassical trajectory calculations based on two reactive potential energy surfaces. In contrast to previous studies with internally excited H2+ and D2+ ions, our results reveal a pronounced isotope effect, favoring the production of CH+ over CD+ across all collision energies, and a significant increase in the absolute rate coefficient of the reaction. Our experimental results agree well with our theoretical calculations for vibrationally relaxed HD+ ions in their lowest rotational states. Published by the American Physical Society 2024

Study of the Potential Energy Surface of Reactions in a System Containing I-Propyl and N-Propyl Radicals

Study of the Potential Energy Surface of Reactions in a System Containing I-Propyl and N-Propyl Radicals

New Full-Dimensional Reactive Potential Energy Surface for the H4 System.

As the most abundant molecule in the universe, collisions involving H2 have important implications in astrochemistry. Collisions between hydrogen molecules also represent a prototype for assessing various dynamic methods for understanding fundamental few-body processes. In this work, we develop a new and highly accurate full-dimensional potential energy surface (PES) covering all reactive channels of the H2 + H2 system, which extends our previously reported H2 + H2 nonreactive PES [J. Chem. Theory Comput., 2021, 17, 6747] by adding 39,538 additional ab initio points calculated at the MRCI/AV5Z level in the reactive channels. The global PES is represented with high fidelity (RMSE = 0.6 meV for a total of 79,000 points) by a permutation invariant polynomial neural network (PIP-NN) and is suitable for studying collision-induced dissociation, single-exchange, as well as four-center exchange reactions. Preliminary quasi-classical trajectory studies on the new PIP-NN PES reveal strong vibrational enhancement of all reaction channels.

Solvent Polarity Effects on the Mechanochemistry of Spiropyran Ring Opening.

The spiropyran mechanophore (SP) is employed as a reporter of molecular tension in a wide range of polymer matrices, but the influence of surrounding environment on the force-coupled kinetics of its ring opening has not been quantified. Here, we report single-molecule force spectroscopy studies of SP ring opening in five solvents that span normalized Reichardt solvent polarity factors (ETN) of 0.1-0.59. Individual multimechanophore polymers were activated under increasing tension at constant 300 nm s-1 displacement in an atomic force microscope. The extension results in a plateau in the force-extension curve, whose midpoint occurs at a transition force f* that corresponds to the force required to increase the rate constant of SP activation to approximately 30 s-1. More polar solvents lead to mechanochemical reactions that are easier to trigger; f* decreases across the series of solvents, from a high of 415 ± 13 pN in toluene to a low of 234 ± 9 pN in n-butanol. The trend in mechanochemical reactivity is consistent with the developing zwitterionic character on going from SP to the ring-opened merocyanine product. The force dependence of the rate constant (Δx‡) was calculated for all solvent cases and found to increase with ETN, which is interpreted to reflect a shift in the transition state to a later and more productlike position. The inferred shift in the transition state position is consistent with a double-well (two-step) reaction potential energy surface, in which the second step is rate determining, and the intermediate is more polar than the product.

On the General Mechanism for the Gas-phase Reaction of Methanimine with a Radical Species in the Interstellar Medium: Some Failures and an Important Success

Abstract The gas-phase reactions of methanimine (CH2NH) with small radicals, such as CN, CP, CCH, and OH, have been extensively studied theoretically in the literature, and the presence of a common, general reaction mechanism has been postulated. Since methanimine is considered the main precursor of complex imines in the interstellar medium (ISM), the present study extends the investigation of its reaction with other small radicals that have already been detected in the ISM. These are SiN, SH, NO, NS, HCO, HCS, and C3N. The corresponding products are easily formulated on the basis of the aforementioned general mechanism, and to understand whether they can be formed in the ISM, a preliminary thermochemical study has been carried out. The only exothermic addition reaction is that occurring between CH2NH and the C3N radical. This reaction has been further investigated in order to accurately characterize its reactive potential energy surface, which has then been employed in ab initio transition state theory calculations to derive global rate coefficients. The products of the CH2NH + C3N reaction are new potential interstellar species, namely, the Z and E isomers of HNCHCCCN and CH2NCCCN. For the first time, their structural characterization has been reported. In addition, this work investigates the possibility of H-abstraction processes for each radical species considered, and re-examines the CH2NH + CP reaction to derive the corresponding rate constants, that were still missing in the literature.

Theoretical study on iso‐pentanol oxidation chemistry: Fuel radical isomerization and decomposition kinetics and mechanism development

AbstractThis study undertakes a detailed theoretical investigation into the iso‐pentanol radical isomerization and decomposition kinetics and the mechanism development of the iso‐pentanol oxidation. The CCSD(T)/CBS//M08‐HX/6‐311+G(2df,2p) method was adopted to calculate the reaction potential energy surface. The reaction rate coefficients were calculated by variational transition state theory (VTST) with multistructural torsional (MS‐T) partition function and small curvature tunneling (SCT) correction. Moreover, the pressure‐dependent rate coefficients were determined using the system‐specific quantum Rice‐Ramsperger‐Kassel theory (SS‐QRRK). The variational and tunneling effects were discussed, and the dominant reaction channels were identified. It reveals that the isomerization reactions play a significant role at low temperatures, while the decomposition reactions dominate the high‐temperature regime. Notably, the quantitative rate expressions for iso‐pentanol radical decomposition reactions were also obtained. Furthermore, a new kinetic model incorporating the calculated rate coefficients was constructed, exhibiting satisfactory prediction performance on ignition delay times and improved predictive accuracy of species mole fractions. This work provides accurate rate data of isomerization and decomposition kinetics and contributes to a more comprehensive understanding of the iso‐pentanol oxidation mechanism.

Benchmark ab initio characterization of the multi-channel Cl + CH3X [X = F, Cl, Br, I] reactive potential energy surfaces.

We determine benchmark geometries and relative energies for the stationary points of the Cl + CH3X [X = F, Cl, Br, I] reactions. We consider four possible reaction pathways: hydrogen abstraction, hydrogen substitution, halogen abstraction, and halogen substitution, where the substitution processes can proceed via either Walden inversion or front-side attack. We perform geometry optimizations and obtain harmonic vibrational frequencies at the explicitly-correlated UCCSD(T)-F12b/aug-cc-pVTZ level of theory, followed by UCCSD(T)-F12b/aug-cc-pVQZ single-point computations to make finite-basis-set error negligible. To reach chemical (<1 kcal mol-1), or even subchemical (<0.5 kcal mol-1) accuracy, we include core-correlation, scalar relativistic, post-(T), spin-orbit-splitting and zero-point-energy contributions, as well, in the relative energies of all the stationary points. Our benchmark 0 K reaction enthalpies are compared to available experimental results and show good agreement. The stationary-point structures and energetics are interpreted in terms of Hammond's postulate and used to make predictions related to the dynamical behavior of these reactive systems.

Hydrogen tunneling with an atypically small KIE measured in the mediated decomposition of the Co(CH3COOH)+ complex.

Quantum mechanical tunneling (QMT) is a well-documented phenomenon in the C-H bond activation mechanism and is commonly identified by large KIE values. Herein we present surprising findings in the kinetic study of hydrogen tunneling in the Co+ mediated decomposition of acetic acid and its perdeuterated isotopologue, conducted with the energy resolved single photon initiated dissociative rearrangement reaction (SPIDRR) technique. Following laser activation, the reaction proceeds along parallel product channels Co(CH4O)+ + CO and Co(C2H2O)+ + H2O. An energetic threshold is observed in the energy dependence of the unimolecular microcanonical rate constants, k(E). This is interpreted as the reacting population surmounting a rate-limiting Eyring barrier in the reaction's potential energy surface. Measurements of the heavier isotopologue's reaction kinetics supports this interpretation. Kinetic signatures measured at energies below the Eyring barrier are attributed to H/D QMT. The below-the-barrier tunneling kinetics presents an unusually linear energy dependence and a staggeringly small tunneling KIE of ∼1.4 over a wide energy range. We explain this surprising observation in terms of a narrow tunneling barrier, wherein the electronic structure of the Co+ metal plays a pivotal role in enhanced reactivity by promoting efficient tunneling. These results suggest that hydrogen tunneling could play important functions in transition metal chemistry, such as that found in enzymatic mechanisms, even if small KIE values are measured.

Navigating the Potential Energy Surface of CdSe Magic-Sized Clusters: Synthesis and Interconversion of Atomically Precise Nanocrystal Polymorphs.

Magic-sized clusters (MSCs) are kinetically stable, atomically precise intermediates along the quantum dot (QD) reaction potential energy surface. Literature precedent establishes two classes of cadmium selenide MSCs with QD-like inorganic cores: one class is proposed to be cation-rich with a zincblende crystal structure, while the other is proposed to be stoichiometric with a "wurtzite-like" core. However, the wide range of synthetic protocols used to access MSCs has made direct comparisons of their structure and surface chemistry difficult. Furthermore, the physical and chemical relationships between MSC polymorphs are yet to be established. Here, we demonstrate that both cation-rich and stoichiometric CdSe MSCs can be synthesized from identical reagents and can be interconverted through the addition of either excess cadmium or selenium precursor. The structural and compositional differences between these two polymorphs are contrasted using a combination of 1H NMR spectroscopy, X-ray diffraction (XRD), pair distribution function (PDF) analysis, inductively coupled plasma optical emission spectroscopy, and UV-vis transient absorption spectroscopy. The subsequent polymorph interconversion reactions are monitored by UV-vis absorption spectroscopy, with evidence for an altered cluster atomic structure observed by powder XRD and PDF analysis. This work helps to simplify the complex picture of the CdSe nanocrystal landscape and provides a method to explore structure-property relationships in colloidal semiconductors through atomically precise synthesis.

Single-atom catalysis in space: Computational exploration of Fischer–Tropsch reactions in astrophysical environments

Context. Gas-phase chemistry at extreme conditions (low densities and temperatures) is difficult, so the presence of interstellar grains is especially important for the synthesis of molecules that cannot form in the gas phase. Interstellar grains are advocated to enhance the encounter rate of the reactive species on their surfaces and to dissipate the energy excess of largely exothermic reactions, but less is known of their role as chemical catalysts that provide low activation energy pathways with enhanced reaction rates. Different materials with catalytic properties are present in interstellar environments, like refractory grains containing space-abundant d-block transition metals. Aims. In this work we report for first time mechanistic insights on the Fischer–Tropsch methanol (CH3OH) synthesis under astrophysical conditions using single-atom Fe-containing silica surfaces as interstellar heterogeneous catalysts. Methods. Quantum chemical calculations considering extended periodic surfaces were carried out in order to search for the stationary points and transitions states to finally construct the reaction potential energy surfaces. Binding energy and kinetic calculations based on the Rice–Ramsperger–Kassel–Marcus (RRKM) scheme were also performed to evaluate the catalytical capacity of the grain and to allocate those reaction processes within the astrochemical framework. Results. Our mechanistic studies demonstrate that astrocatalysis is feasible in astrophysical environments. Thermodynamically the proposed process is largely exergonic, but kinetically it shows energy barriers that would need from an energy input in order to go through. Kinetic calculations also demonstrate the strong temperature dependency of the reaction process as tunnelling is not relevant in the involved energetic barriers. The present results can explain the presence of CH3OH in diverse regions where current models fail to reproduce its observational quantity. Conclusions. The evidence of astrocatalysis opens a completely new spectrum of synthetic routes triggering chemical evolution in space. From the mechanistic point of view the formation of methanol catalysed by a single atom of Fe0 is feasible; however, its dependency on the temperature makes the energetics a key issue in this scenario.

The conversion mechanism of syngas CO and H2 under Au and Au-CCo-doping catalysts

The relative stability, reaction potential energy surface, NBO charge analysis and kinetic properties of Au, Au-C co-doping catalysts in CO and H2 syngas catalytic reactions were studied by density functional theory calculation. The calculation results indicate that the reaction energy barrier and reaction rate showed a consistent pattern of change. NBO charge analysis indicates the feasibility of the catalytic reaction of syngas. We also calculated the rate constant which indicates that the rate constant has a positive temperature dependence. Our calculations show that the reaction is an exothermic reaction catalyzed by Au and Au-C co-doping.

A Gaussian Process Based Δ-Machine Learning Approach to Reactive Potential Energy Surfaces.

The Gaussian process (GP) is an efficient nonparametric machine learning (ML) method. A distinct advantage of the GP is its ability to provide an estimate of statistical uncertainties. This is particularly useful in constructing high-dimensional potential energy surfaces (PESs) from ab initio data as it offers an optimal way to add new geometries to reduce the overall error. In this work, GP is employed in the context of Δ-machine learning (Δ-ML), in which a correction PES to an inaccurate low-level PES is constructed using a small number of high-level ab initio calculations. This new method is tested in three prototypical reactive systems, namely, the H + H2 → H + H2, OH + H2 → H2O + H, and H + CH4 → H2 + CH3 reactions. The results show that the GP-based Δ-ML approach is more efficient than its direct application in constructing high-level PESs. We also compare the new method to a previously proposed neural-network-based Δ-ML approach [Liu and Li J. Phys. Chem. Lett. 2022, 13, 4729-4738]. The results indicate that the two Δ-ML methods have comparable efficiencies in constructing accurate PESs.

Study on the methane dehydrogenation reaction catalyzed by triangular transition metal: a theoretical research

The relative stability, reaction potential energy surface, naturally bonded orbit (NBO) charge analysis, and kinetic properties of triangular transition metal catalysts in methane dehydrogenation reaction were studied by density functional theory calculation. The calculation results indicate that the process of triangular metal adsorption of methane is physical adsorption, and the main products of the reaction are hydrogen and carbon-based materials. This reaction is a multicomponent reaction. NBO charge analysis indicates the feasibility of the catalytic reaction of methane dehydrogenation. We also calculated the rate constant which indicates that the rate constant has a positive temperature dependence. Our calculations show that the reaction is an exothermic reaction catalyzed by triangular transition metal catalyzer.