Related Transition States Research Articles

Density Functional Theory Study of the Hydrogenation of Carbon Monoxide over the Co (001) Surface: Implications for the Fischer–Tropsch Process

The increasing demand for renewable fuels and sustainable products has encouraged growing interest in the development of active and selective catalysts for the conversion of carbon monoxide into desirable products. The Fischer–Tropsch process consists of the reaction of a synthesis gas mixture containing carbon monoxide and hydrogen (syngas), which are polymerized into liquid hydrocarbon chains, often using a cobalt catalyst. Here, first-principles calculations based on the density functional theory (DFT) are used to investigate the reaction mechanism of the Fischer–Tropsch synthesis over the Co (001) surface. The most energetically favorable adsorption configurations of the species involved in the carbon monoxide hydrogenation process are identified, and the possible elementary steps of hydrogenation and their related transition states are explored using the Vienna Ab initio simulation package (VASP). The results provide the mechanisms for the formation of CH4, CH3OH and C2H2 compounds, where the calculations suggest that CH4 is the dominant product. Findings from the reaction energies reveal that the preferred mechanism for the hydrogenation of carbon monoxide is through HCO and cis-HCOH, and the largest exothermic reaction energy in the CH4 formation pathway is released during the hydrogenation of cis-HCOH (−0.773 eV). An analysis of the kinetics of the hydrogenation reactions indicates that the CH production from cis-HCOH has the lowest energy barrier of just 0.066 eV, and the hydrogenation of CO to COH, with the largest energy barrier of 1.804 eV, is the least favored reaction kinetically.

Theoretical study on the free radical scavenging potency and mechanism of natural coumestans: Roles of substituent, noncovalent interaction and solvent

The free radical scavenging potency and mechanisms of seven representative natural coumestans were systematically evaluated using density functional theory (DFT) approach. Thermodynamic feasibility of different mechanisms was assessed by various physio-chemical descriptors involved in the double (2H+/2e‒) radical-trapping processes. Energy diagram and related transition state structures of the reaction between wedelolactone (WEL) and hydroperoxyl radical were constructed to further uncover the radical-trapping details. Results showed that the studied coumestans prefer to scavenge radicals via formal hydrogen atom transfer (fHAT) mechanism in the gas phase and non-polar environment, whereas sequential proton loss electron transfer (SPLET) is favored in polar media. Moreover, the feasibility of second fHAT and SPLET processes was also revealed. Sequential double proton loss double electron transfer (SdPLdET) mechanism represents the preferred pathway in aqueous solution at physiological pH. Our findings highlight the essential role of ortho-dihydroxyl group, noncovalent interaction and solvents on radical-trapping potency. 4′-OH in D-ring was found to be the most favorable site to trap radical for most of the studied coumestans, whereas 3-OH in A-ring for lucernol (LUN).

Paying Comprehensive Attention to the ESPT Mechanism and Luminescent Property of Salicylic Acid and Its Derivatives in Various Microenvironments

AbstractInvestigating the effects of surrounding microenvironments and substituents on the excited‐state proton transfer (ESPT) mechanism have always been a great challenge, especially in protic solvents and solid state. In this work, a detailed theoretical study on ESPT processes of salicylic acid (SA) and its two derivatives (5ASA and 5NSA) in gas, cyclohexane, acetonitrile, ethanol (EtOH), and crystal phases is performed based on the density functional theory (DFT) and time‐dependent DFT as well as the combined quantum mechanics/molecular mechanics (QM/MM) methods. Intramolecular charge transfer‐induced aggregation‐caused quenching phenomenon of 5ASA is unveiled utilizing the hole–electron analysis. Independent gradient model analysis is implemented to reveal the spontaneous forward proton transfer (PT) behavior of 5ASA. Besides, potential energy surfaces are constructed to evaluate the dominant PT pathway in EtOH, and the related transition state structures are also obtained to accurately provide the intra‐ and inter‐PT energy barriers. Eventually, excited‐state ab initio molecular dynamics computation reaffirms that the intra‐PT reaction is predominant for SA. This theoretical work comprehensively explores the ESPT mechanism and luminescent properties of SA and its two derivatives, which provides a reference for developing efficient organic light‐emitting materials based on ESPT chromophores.

Product specific thermal degradation kinetics of bisphenol F epoxy in inert and oxidative atmospheres using evolved gas analysis–mass spectrometry

Knowledge of the degradation kinetics for polymer materials is important for understanding thermal stability. Here, evolved gas analysis–mass spectrometry and pyrolysis gas-chromatography-mass spectrometry were evaluated for the potential to deliver additional insight into thermal degradation kinetics of diglycidal ether of bisphenol F (DGEBF) epoxy thermoset under inert and oxidative atmospheres. Degradation products of selected precursor ions were evaluated for their uniqueness to the specific precursor using extracted ion thermographs. Unique mass peaks, solely attributed to a single reaction pathway of a specific product, were determined from extracted ion thermographs and used to determine both activation energy (Ea) and pre-exponential factors for the specific primary reaction pathways. These primary reaction pathways for DGEBF epoxy degradation were then evaluated in the context of transition state theory (TST) and related transition state enthalpies (ΔH‡) and entropies (ΔS‡) of activation to further elucidate the degradation process. It was determined under pyrolysis conditions, as suggested by the Ea, the formation of bisphenol F monomer was the rate-limiting step toward the formation of xanthene and phenol. In contrast, under thermo-oxidative conditions, reactions involving oxygen containing species were identified as the rate-limiting step for all observed products based on the large negative ΔS‡ calculated from TST. This work demonstrates a powerful combination of technique and theory that can provide new insight into the degradation of polymer materials.

Inverse α-Effect as the Ariadne's Thread on the Way to Tricyclic Aminoperoxides: Avoiding Thermodynamic Traps in the Labyrinth of Possibilities.

Stable tricyclic aminoperoxides can be selectively assembled via a catalyst-free three-component condensation of β,δ'-triketones, H2O2, and an NH-group source such as aqueous ammonia or ammonium salts. This procedure is scalable and can produce gram quantities of tricyclic heterocycles, containing peroxide, nitrogen, and oxygen cycles in one molecule. Amazingly, such complex tricyclic molecules are selectively formed despite the multitude of alternative reaction routes, via equilibration of peroxide, hemiaminal, monoperoxyacetal, and peroxyhemiaminal functionalities! The reaction is initiated by the "stereoelectronic frustration" of H2O2 and combines elements of thermodynamic and kinetic control with a variety of mono-, bi-, and tricyclic structures evolving under the conditions of thermodynamic control until they reach a kinetic wall created by the inverse α-effect, that is, the stereoelectronic penalty for the formation of peroxycarbenium ions and related transition states. Under these conditions, the reaction stops before reaching the most thermodynamically stable products at a stage where three different heterocycles are assembled and fused at the acyclic precursor frame.

Versatile Fe-Sn Bonding Interactions in a Metallostannylene System: Multiple Bonding and C-H Bond Activation.

The metallostannylene Cp*(iPr2MeP)(H)2Fe-SnDMP (1; Cp* = η5-C5Me5; DMP = 2,6-dimesitylphenyl), formed by hydrogen migration in a putative Cp*(iPr2MeP)HFe[Sn(H)DMP] intermediate, serves as a robust platform for exploration of transition-metal main-group element bonding and reactivity. Upon one-electron oxidation, 1 expels H2 to generate the coordinatively unsaturated [Cp*(iPr2MeP)Fe═SnDMP][B(C6F5)4] (3), which possesses a highly polarized Fe-Sn multiple bond that involves interaction of the tin lone pair with iron. Evidence from EPR and 57Fe Mössbauer spectroscopy, along with DFT studies, shows that 3 is primarily an iron-based radical with charge localization at tin. Upon reduction of 3, C-H bond activation of the phosphine ligand was observed to produce Cp*HFe(κ2-(P,Sn)═Sn(DMP)CH2CHMePMeiPr) (5). Complex 5 was also accessed via thermolysis of 1, and kinetics studies of this thermolytic pathway indicate that the reductive elimination of H2 from 1 to produce a stannylyne intermediate, Cp*(iPr2MeP)Fe[SnDMP] (A), is likely rate-determining. Evidence indicates that the production of 5 proceeds through a concerted C-H bond activation. DFT investigations suggest that the transition state for this transformation involves C-H cleavage across the Fe-Sn bond and that a related transition state where C-H bond activation occurs exclusively at the tin center is disfavored, illustrating an effect of iron-tin cooperativity in this system.

Molecular structure and electronic properties of substituted tetrabenzocoronenes: DFT and TD‐DFT investigations

Abstract1,2:3,4:7,8:9,10‐Tetrabenzocoronene (TBC) is a highly π‐conjugated polycyclic aromatic hydrocarbon (PAH) with an intriguing nonplanar, twisted molecular shape featuring two [4]helicene subunits on the opposite sides of the molecule. In this study, we examined the electronic substituent effects on the molecular properties of a series of TBC derivatives by density functional theory (DFT) and time‐dependent DFT (TD‐DFT) computational analysis at the B3LYP/6‐31G(d) and TD‐B3LYP/6‐311 + G(d,p) levels. The equilibrium geometries for the stable conformers of the TBC derivatives in the ground singlet state (So) and related transition states were optimized to obtain the energy barriers associated with the interconversion among these conformers. Variations of aromatic character for these compounds were evaluated by nucleus‐independent chemical shift (NICS) calculations, while the frontier molecular orbital (FMO) energies and the vertical electronic absorption and emission energies were calculated. The calculated absorption and emission spectra of these TBC derivatives show good correlations with the Hammett substituent constant (σ). Overall, our study has demonstrated that the attachment of electron‐donating/withdrawing substituents to the edges of TBC can exert significant effects on the structural, electronic, and photophysical properties. Understanding of the substitution effects on TBC provides valuable insight for the design and development of novel PAH‐based organic electronic materials and devices.

Transition of Metastable Cross-α Crystals into Cross-β Fibrils by β-Turn Flipping.

The ensemble of native, folded state was once considered to represent the global energy minimum of a given protein sequence. More recently, the discovery of the cross-β amyloid state revealed that deeper energy minima exist, often associated with pathogenic, fibrillar deposits, when the concentration of proteins reaches a critical value. Fortunately, a sizable energy barrier impedes the conversion from native to pathogenic states. However, little is known about the structure of the related transition state. In addition, there are indications of polymorphism in the amyloidogenic process. Here, we report the first evidence of the conversion of metastable cross-α-helical crystals to thermodynamically stable cross-β-sheet-like fibrils by a de novo designed heptapeptide. Furthermore, for the first time, we demonstrate at atomic resolution that the flip of a peptide plane from a type I to a type II' turn facilitates transformation to cross-β structure and assembly of a dry steric zipper. This study establishes the potential of a peptide turn, a common protein secondary structure, to serve as a principal gatekeeper between a native metastable folded state and the amyloid state.

Exploring the methanol decomposition mechanism on the Pt3Ni(100) surface: a periodic density functional theory study.

The detailed mechanism of the methanol decomposition reaction (MDR) on the Pt3Ni(100) surface is studied based on self-consistent periodic density functional theory calculations. The geometries and energies of methanol and its intermediates involved in MDR are analyzed, and the reaction network is constructed to illustrate the MDR mechanisms. The possible pathways through initial scission of the O-H, C-H, and C-O bonds in methanol are discussed based on the steric effect and electronic structure of the related transition states and the Brønsted-Evans-Polanyi (BEP) relationships. The initial scission of the O-H bond is favorable and bears the lowest energy barrier among the three decomposition modes (initial scission of O-H, C-H, and C-O bonds). Potential energy surface (PES) analysis confirmed that although the initial scission of the O-H bond is more favorable than scission of the C-H bond, the initial scission of the C-H bond can actually occur because of the very low energy barrier for further dehydrogenation of CH2OH via scission of its O-H bond. Thus, the pathway for MDR on the Pt3Ni(100) surface may possibly proceed via two competitive pathways: CH3OH → CH3O → CH2O → CHO → CO and CH3OH → CH2OH → CH2O → CHO → CO. Comparisons between the current results and the MDR on other systems are made and show that Pt3Ni(100) can be a good catalyst for MDR.

Mechanism of Methanol Decomposition on the Pt3Ni(111) Surface: DFT Study

This work reports the detailed mechanism of methanol decomposition on Pt3Ni(111) based on self-consistent periodic density functional theory calculations. The geometries and energies of methanol and its intermediates are analyzed, and the decomposition network is mapped to illustrate the decomposition reaction mechanisms. On Pt3Ni(111), the less electronegative Ni atoms are more favorable for adsorbing radical intermediates and intermediates with lone-pair electrons (such as O-containing species). The possible pathways through initial scission of the O–H, C–H, and C–O bonds in methanol are studied and discussed based on the steric effect and electronic structure of the related transition states and the Bronsted-Evans–Polanyi (BEP) relationships. The initial scission of the O–H bond is the most favorable and bears the lowest energy barrier among the three decomposition modes (initial scission of O–H, C–H, and C–O bonds). The decomposition of the energy barrier analysis indicates that the high energy barrie...

Theoretical Investigation on the Kinetics and Mechanism of the Synthesis of Fluorescent 3,8-Disubstituted-3H-Imidazo [4,5-a] Acridine-11-Carbonitriles

3,8-Disubstituted-3H-imidazo[4,5-a]acridine-11-carbonitriles show very interesting optical properties. In some cases, they have higher quantum yields compared to well-known fluorescent dyes such as fluorescein. Hitherto, no detailed theoretical study has been reported on the mechanism of the synthesis of the titled compounds, hence an accurate and detailed theoretical investigation on the synthesis of these dyes is desirable. In this paper, density functional theory (DFT) methods have been employed to investigate the most reasonable mechanism in formation of these fluorophores. All species and related transition states were optimised and the relative energies of all species and the activation energies for all proposed mechanisms were obtained. Comparing the Ea values of all pathways reveals that intramolecular electrophilic aromatic substitution is the most plausible mechanism for the cyclisation reaction in the preparation of these dyes. Also, the effects of substituents in positions 3 and 8 were investigated and the results show that electron-donor substituents can reduce the activation energy for formation of the σ complex in the electrophilic aromatic substitution.

Vibrational memory in quantum localized states

The rovibrational eigenenergy set of molecular systems is a key feature needed to understand and model elementary chemical reactions. A unique class of molecular systems, represented by an ${}^{4}{A}^{\ensuremath{'}\ensuremath{'}}$ excited electronic state of the ${[\mathrm{H},\mathrm{S},\mathrm{N}]}^{\ensuremath{-}}$ system comprising several distinct dipole-bound isomers, is found to contain both bent and linear minima separated by relatively small barriers. Full-dimensional nuclear-motion computations performed in Jacobi coordinates using three-dimensional potential energy surfaces describing the stable isomers and the related transition states yield rovibrational eigenstates located both below and above the barriers. The rovibrational wave functions are well localized, regardless of whether the state's energy is below or above the barriers. We also show that the states preserve the memory of the isomeric forms they ``originate from,'' which is signature of a strong vibrational memory effect above isomerization barriers.

Density functional theory study of C₂F₅I synthesis over activated carbon catalyst.

Quantum chemistry calculations based on the density functional theory (DFT) are carried out to investigate the reaction mechanism of C2F5I synthesis catalyzed by activated carbon. The possible adsorption configurations of fluorocarbon intermediates are analyzed carefully. Also, the related transition states and reaction pathway are analyzed. According to calculation, firstly, the dehydrofluorination of C2HF5, as the rate-determining step, is catalyzed by the carboxyl acid groups. Secondly, the tetrafluoroethylidene radicals disproportionate on graphite (001) surface instead of rearrangement or dimerization. Next, the fluorine abstractions between fluorocarbon intermediates over graphite (001) surfaces proceed successfully. Finally, the desorbed pentafluoroethyl abstracts iodine atom from molecular iodine spontaneously to afford C2F5I. In adition, our calculations reveal that the carbon deposit in experiment is caused by the fluorine abstraction from fluoroethinyl. The suggested mechanism corresponds with our calculations and available experiments.

Weakly nucleophilic potassium aryltrifluoroborates in palladium-catalyzed Suzuki-Miyaura reactions: relative reactivity of K[4-RC6F4BF3] and the role of silver-assistance in acceleration of transmetallation.

Small differences in the reactivity of weakly nucleophilic potassium aryltrifluoroborates are revealed in the silver-assisted Pd-catalyzed cross-coupling of K[4-RC6F4BF3] (R = H, Bu, MeO, EtO, PrO, iPrO, BuO, t-BuO, CH2=CHCH2O, PhCH2O, PhCH2CH2O, PhO, F, pyrazol-1-yl, pyrrol-1-yl, and indol-1-yl) with ArX (4-BrC6H4CH3, 4-IC6H4F and 3-IC6H4F). An assumed role of silver(I) compounds AgmY (Y = O, NO3, SO4, BF4, F) consists in polarization of the Pd–X bond in neutral complex ArPdLnX with the generation of the related transition state or formation of [ArPdLn][XAgmY] with a highly electrophilic cation and subsequent transmetallation with the weakly nucleophilic borate. Efficiency of AgmY as a polarizing agent decreases in order Ag2O > AgNO3 ≈ Ag2SO4 > Ag[BF4] > AgF. No clear correlation between the reactivity of K[4-RC6F4BF3] and substituent electron parameters, σI and σR°, of the aryl group 4-RC6F4 was found.

Photoexcitation and photoionization of alkali atoms

The dynamical process of photoexcitation and photoionization of alkali atoms is studied with three-step laser pulses, focusing on the similarities and differences between Li and Cs atoms on their properties by making a comparison of them. Based on several excitation schemes, the present work not only establishes the rate equations of atom population for all related transition states, but also obtains the analytical solutions of photoexcitation and photoionization process. The mathematical solutions are simplified significantly by restricting the most general case to the several special cases, either designed or selected carefully, in order to highlight the main factors and obtain the physical insight underlying the complicated mathematical expressions. With self-programming, the possible impact of time configuration of laser pulses on the three-step laser excitation process of the photoexcitation and photoionization is calculated and studied systematically. Variation of the ionization efficiency with the laser parameters is investigated and discussed. With the same time configuration of laser pulses, the dependences of atom population for all the related transition states on the two different excitation paths are compared and analyzed, reflecting the impact of changing the atomic parameters. Under the similar excitation conditions, the differences of ionization efficiency between Li and Cs atoms are explored. Finally, based on the present study, several means for optimizing ionization efficiency are proposed.

Insights into the mechanism of heterogeneous mercury oxidation by HCl over V2O5/TiO2 catalyst: Periodic density functional theory study

The selective catalytic reduction (SCR) for the reduction of NOx can enhance the oxidation of elemental mercury, which is regarded as a low-cost option for mercury control in coal-fired power plants. First-principles calculations based on the density functional theory and the periodic slab models were used to gain a fundamental understanding of mercury oxidation mechanism across V2O5/TiO2 SCR catalyst. The adsorption of Hg0, HCl, HgCl, and HgCl2 on V2O5/TiO2(001) surface were studied. The energy profile of the oxidation reaction and the structures of related transition states and intermediates were examined. The results show that Hg0 is mainly physically absorbed on vanadyl–oxygen sites of the V2O5/TiO2(001) surface with an adsorption energy of −27.93kJ/mol. HCl is chemisorbed on vanadyl–oxygen sites of V2O5/TiO2(001) surface, and can undergoes dissociation process with an energy barrier of 101.53kJ/mol to form the vanadium oxy-chloride complex which is essential in Hg0 oxidation reaction on V2O5/TiO2(001) surface. The mercury oxidation reaction occurs through an Eley–Rideal mechanism in which Hg reacts with HCl that has previously been adsorbed and dissociated on V2O5/TiO2(001) surface to form surface HgCl, and then surface HgCl reacts with HCl to form HgCl2, finally HgCl2 desorbs from the V2O5/TiO2(001) surface. In the whole Hg oxidation reaction, the formation of HgCl2 is the rate-determining step based on its high energy barrier.

CF3I Synthesis Catalyzed by Activated Carbon: A Density Functional Theory Study

A revised reaction mechanism of CF3I synthesis catalyzed by activated carbon is investigated with quantum chemistry methods using density functional theory (DFT). The adsorption configurations of possible intermediates are carefully examined. The reaction pathway and related transition states are also analyzed. According to our calculations, first, the dehydrofluorination of CHF3 is catalyzed by -COOH groups, which possesses the highest barrier and is accordingly identified as the rate-determining step. Second, the difluorocarbene disproportionation over graphite (001) surface proceeds instead of dimerization. The next reaction steps involving the association of fluoromethine and trifluoromethyl, the fluorine abstractions between intermediates and the iodine abstractions by the desorbed CF3 and CF2CF3 from molecular iodine are also feasible over graphite (001) surfaces. It is also found that the coke deposition in experiments is due to the fluorine abstraction from fluoromethine. This revised mechanism is in agreement with available experimental data and our theoretical computations.

Mercury oxidation mechanism on Pd(1 0 0) surface from first-principles calculations

Pd-based sorbents have been considered as potential promising sorbents for Hg capture because of their regeneration and high activity over long times. First-principles calculations based on the density functional theory and the periodic slab models were used to gain a fundamental understanding of mercury oxidation mechanism on Pd(100) surface. The adsorptions of Hg0, HCl, HgCl, and HgCl2 on the Pd(100) surface were studied. The electronic structural changes of surface system before and after adsorption were investigated to better understand the surface reactivity. The energy profile of the oxidation reaction and the structures of related transition states and intermediates were examined. The results show that Hg0 is strongly adsorbed on hollow site of the surface with a chemisorption mechanism. HCl is chemisorbed on Pd(100) surface by side-on orientation, and its dissociation occurs with a low energy barrier, and this process is exothermic. The adsorptions of HgCl and HgCl2 are mainly chemisorption. The mercury oxidation reaction on Pd(100) surface occurs through a Langmuir–Hinshelwood mechanism in which Hg adsorbs and then reacts with HCl that has previously been adsorbed and dissociated on the Pd(100) surface.

Quantum chemical studies of photochromic properties of benzoxazine compound

Molecular electronic structure of ground and excited states of a photochromic indolo[2,1-b][1,3]benzoxazine compound incorporating closed-ring system, which opens upon UV light excitation, was studied using various quantum chemical methods. Three local minima of the ground electronic state potential energy surface and related transition states were identified along the path of rotation of 4-nitrophenol group. Additionally, three local minima of the excited electronic states were located. The evaluated transition energy barriers between local ground-state minima nearest to the initial structure of the investigated molecule are less than 2 kBT, making open structures likely to revert to the initial structure by thermalization. Results obtained using ab initio GMC–QDPT method were explored and compared to the widely used TD-DFT and semi-empiric ZINDO methods.

Ethanol Reforming on Co(0001) Surfaces: A Density Functional Theory Study

A computational study using density functional theory is carried out to investigate the reaction mechanism of ethanol steam reforming on Co(0001) surfaces. The adsorption properties of the reactant, possible intermediates, and products are carefully examined. The reaction pathway and related transition states are also analyzed. According to our calculations, the reforming mechanism primarily consisting of dehydrogenation steps of ethanol, ethoxy, methanol, methoxy, and formic acid, is feasible on Co(0001) surfaces. It is also found that the reaction of formaldehyde yielding formic acid and hydrogen may not be an elementary reaction. The dehydrogenation of ethoxy possesses the highest barrier and is accordingly identified as the rate-determining step.