Low Reaction Barrier Research Articles

The highly effective catalytic behavior of a metal nanocluster Ru79 on the dissociation of a N2 molecule—A quantum-chemical calculation

Density-functional theory calculations for the N2 molecule dissociation on a twinned truncated octahedral (t-TO) Ru79 nanocluster have been investigated. Results demonstrate that dissociating the NN bond of a N2 molecule on a t-TO Ru79 nanocluster has a very low reaction barrier, 0.27eV. An analysis of the charge indicates that the direction of the 2π* orbital of the adsorbed N2 molecule is parallel to the close-packed Ru atoms on a valley-like active site composed of seven Ru atoms, inducing much transfer of charge from the d orbital of Ru atoms to the 2π* orbital, so producing this small barrier.

Acid catalyzed first dehydration of glycerol at the secondary site: The effect of glycerol conformation

The first dehydration of protonated glycerol taking place at its secondary site was investigated by density functional calculations by considering different conformations of glycerol. Five parallel reaction pathways via different conformers of protonated glycerol were found. One of these pathways leads to a direct formation of protonated 3-hydroxylpropanal (HPA), another one of these pathways produces protonated glycidol, and the other three produce protonated 3-hydroxy-1,1-propanediol (HPD). One of these pathways producing protonated HPD was found to have obviously larger relative reaction rate than other pathways. The dehydration of protonated HPD to afford protonate HPA requires a rather low reaction barrier (12 kcal/mol). These results show that the production of HPA via a stepwise process with protonated HPD as a key intermediate, is energetically favorable than via a one-step concerted process producing HPA.

Disclosure of Key Stereoelectronic Factors for Efficient H2 Binding and Cleavage in the Active Site of [NiFe]-Hydrogenases

A comparative analysis of a series of DFT models of [NiFe]-hydrogenases, ranging from minimal NiFe clusters to very large systems including both the first and second coordination sphere of the bimetallic cofactor, was carried out with the aim of unraveling which stereoelectronic properties of the active site of [NiFe]-hydrogenases are crucial for efficient H2 binding and cleavage. H2 binding to the Ni-SIa redox state is energetically favored (by 4.0 kcal mol(-1)) only when H2 binds to Ni, the NiFe metal cluster is in a low spin state, and the Ni cysteine ligands have a peculiar seesaw coordination geometry, which in the enzyme is stabilized by the protein environment. The influence of the Ni coordination geometry on the H2 binding affinity was then quantitatively evaluated and rationalized analyzing frontier molecular orbitals and populations. Several plausible reaction pathways leading to H2 cleavage were also studied. It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies. More importantly, the seesaw coordination geometry of Ni was found to be a key feature for facile H2 cleavage. The discovery of the crucial influence of the Ni coordination geometry on H2 binding and activation in the active site of [NiFe]-hydrogenases could be exploited in the design of novel biomimetic synthetic catalysts.

Inorganic acid-catalyzed tautomerization of vinyl alcohol to acetaldehyde

The vinyl alcohol–acetaldehyde tautomerization reaction has recently received considerable attention as a potential route for the formation of organic acids in the troposphere (Andrews et al., 2012 [7]). We examine the catalytic effect of inorganic acids in the troposphere (e.g. HNO3, H2SO4 and HClO4) on the vinyl alcohol–acetaldehyde tautomerization reaction, by means high-level thermochemical procedures. We show that H2SO4 and HClO4 catalysts lead to near-zero reaction barrier heights for the vinyl alcohol→acetaldehyde reaction, and to low reaction barrier heights in the reverse direction (ΔH298‡=40.6and39.5kJmol-1, respectively).

A density functional theory study on oxygen reduction reaction on nitrogen-doped graphene

Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and the transition state of each elementary step was identified. The results showed that OOH reduction was easier than O-OH breaking. OOH reduction followed a direct Eley-Rideal mechanism (the OOH species was in gas phase, but H was chemisorbed on the surface) with a significantly low reaction barrier of 0.09 eV. Pathways for both four-electron and two-electron reductions were possible. The rate-determining step of the two-electron pathway was the reduction of O₂ (formation of OOH), whereas that of the four-electron pathway was the reduction of OH into H₂O. After comparing the barriers of the rate-determining steps of the two pathways, we found that the two-electron pathway was more energetically favored than the four-electron pathway.

Nitrogen-containing carbon nanostructures: A promising carrier for catalysis of ammonia borane dehydrogenation

The first-principles calculations demonstrate that nitrogen-containing carbon nanostructures (NCCN), such as nitrogen-doped graphene, nitrogen-doped carbon nanotubes, and covalent triazine-based framework (CTF) are promising metal-free catalysts for the first step dehydrogenation of ammonia borane (AB). It reveals that nitrogen lone pairs in NCCN function as hydrogen acceptors to allow metal-free hydrogen transfer from AB to NCCN, resulting in facile release of pure H2 from AB. The dehydrogenation of AB–NCCN combined systems involves two key steps: First, there is a net transfer of hydrogen atoms from AB to NCCN that results in simultaneous dehydrogenation of AB and hydrogenation of the NCCN, and then, the hydrogenated NCCN further react with AB to release H2 with relatively low reaction barriers. The experimental results further confirm that the CTF can act as effective catalysts for AB dehydrogenation at relatively low temperature. Our study leads to a promising scheme that can be readily tailored for application to many nitrogen-containing nanostructure systems that may favorably catalyze the dehydrogenation of ammonia borane and other related boron–nitrogen species.

Ab Initio Study of CO2 Capture Mechanisms in Aqueous Monoethanolamine: Reaction Pathways for the Direct Interconversion of Carbamate and Bicarbonate

Ab initio molecular orbital calculations combined with the polarizable continuum model (PCM) formalism have been carried out for a comprehensive understanding of the mechanism of carbon dioxide (CO2) absorption by aqueous amine solutions. CO2 is captured by amines to generate carbamates and bicarbonate. We have examined the direct interconversion pathways of these two species (collectively represented by a reversible hydrolysis of carbamate) with the prototypical amine, monoethanolamine (MEA). We evaluate both a concerted and a stepwise mechanism for the neutral hydrolysis of MEA carbamate. Large activation energies (ca. 36 kcal/mol) and lack of increase in catalytic efficiency with the inclusion of additional water molecules are predicted in both the mechanisms. We also examined the mechanism of alkaline hydrolysis of MEA carbamate at high concentrations of amine (high pH). The addition of OH(-) ion to carbamate anion was theoretically not allowed due to the reduction in the nucleophilicity of the former as a result of microsolvation. We propose an alternative pathway for hydrolysis: a proton transfer from protonated MEA to carbamate to generate the carbamic acid that initially undergoes a nucleophilic addition of OH(-) and subsequent low-barrier reactions leading to the formation of bicarbonate and free MEA. On the basis of the calculated activation energies, this pathway would be the most efficient route for the direct interconversion of carbamate and bicarbonate without the intermediacy of the free CO2, while the actual contributions will be dependent on the concentrations of protonated MEA and OH(-) ions.

Unusual Magnetic Properties of Functionalized Graphene Nanoribbons

The edge-induced magnetism of graphene nanoribbons (GNRs) has been found to be highly unstable at room temperature, thus making it difficult for spintronics applications under ambient conditions. Using first-principles calculations, we propose a way to overcome this problem by embedding transition-metal atoms into functionalized GNRs. We show that due to low or vanishing reaction barriers, 3d transition-metal atoms can be easily embedded into GNR once they are functionalized by −F or −CN groups. A systematic study of these materials shows fascinating magnetic properties; Co-embedded systems not only have high magnetic anisotropy energies hundreds of times larger than that of pure GNR and bulk Co, but also, the magnetic preferential directions can be switched by an electric field. Mn-embedded systems exhibit giant magnetic moments and half-metallicity with greatly enhanced stability. Under a small amount of biaxial strain, the magnetic moment of every Mn atom in such a Mn-embedded system can be increased by 2.1 μB due to a change in the dxy orbital occupancy, and its Curie temperature is estimated to be over 1000 K.

Bis(sulfonylimide)ruthenium(VI) Porphyrins: X‐ray Crystal Structure and Mechanism of CH Bond Amination by Density Functional Theory Calculations

The X-ray crystal structure of [Ru(VI) (NMs)2 (tmp)] (Ms=SO2 - p-MeOC6 H4 ; tmp=5,10,15,20-tetramesitylporphyrinato(2-)), a metal sulfonylimide complex that can undergo alkene aziridination and C-H bond amination reactions, shows a Ru=N distance of 1.79(3) Å and Ru-N-S angle of 162.5(3)°. Density functional theory (DFT) calculations on the electronic structures of [Ru(VI) (NMs)2 (tmp)] and model complex [Ru(VI) (NMs)2 (por(0) )] (por(0) =unsubstituted porphyrinato(2-)) using the M06L functional gave results in agreement with experimental observations. For the amination of ethylbenzene by the singlet ground state of [Ru(VI) (NMs)2 (por(0))], DFT calculations using the M06L functional revealed an effectively concerted pathway involving rate-limiting hydrogen atom abstraction without a distinct radical rebound step. The substituent effect on the amination reactivity of ethylbenzene by [Ru(VI) (NX)2 (por(0) )] (X=SO2 -p-YC6 H4 with Y=MeO, Me, H, Cl, NO2 ) was examined. Electron-withdrawing Y groups lower the energy of the LUMOs of [Ru(VI) (NX)2 (por(0))], thus facilitating their interaction with the low-lying HOMO of the ethylbenzene C-H bond and hence increasing the reactivity of [Ru(VI) (NX)2 (por(0) )]. DFT calculations on the amination/aziridination reactions of [Ru(VI) (NSO2 C6 H5 )2 (por(0) )] with pent-4-enal, an aldehyde substrate bearing acyl, homoallylic, and allylic C-H bonds and a C=C bond, revealed a lower reaction barrier for the amination of the acyl C-H bond than for both the amination of the other C-H bonds and aziridination of the C=C bond in this substrate.

Intermetallic NaAu2 as a Heterogeneous Catalyst for Low-Temperature CO Oxidation

The enhanced stability and modified electronic structure of intermetallic compounds provide discovery of superior catalysts for chemical conversions with high activity, selectivity, and stability. We find that the intermetallic NaAu2 is an active catalyst for CO oxidation at low temperatures. From density functional theory calculations, a reaction mechanism is suggested to explain the observed low reaction barrier of CO oxidation by NaAu2, in which a CO molecule reacts directly with an adsorbed O2 to form an OOCO* intermediate. The presence of surface Na increases the binding energy of O2 and decreases the energy barrier of the transition states.

Noyori Hydrogenation: Aromaticity, Synchronicity, and Activation Strain Analysis

By means of density functional theory calculations, we have computationally explored the intimacies of the crucial step of Noyori hydrogrogenation reactions of multiple bonds. This process can be considered analogous to the so-called double group transfer reactions. Both kinds of transformations proceed concertedly via the simultaneous migration of two hydrogen atoms/groups in a pericyclic [σ2s + σ2s + π2s] reaction through six-membered transition structures. Despite the structural resemblances of both types of saddle points, significant differences are found in terms of synchronicity and in-plane aromaticity. In addition, the activation strain model has been used to get quantitative insight into the factors which control the corresponding barrier heights. It is found that the presence of a heteroatom in the acceptor moiety is responsible for a remarkable increase of the interaction energy between the reactants which can compensate the destabilizing effect of the strain energy associated with the deformation of the initial reagents leading to low reaction barriers.

Mechanism and Origins of Selectivity in Ru(II)-Catalyzed Intramolecular (5+2) Cycloadditions and Ene Reactions of Vinylcyclopropanes and Alkynes from Density Functional Theory

The mechanism, solvent effects, and origins of selectivities in Ru(II)-catalyzed intramolecular (5+2) cycloaddition and ene reaction of vinylcyclopropanes (VCPs) and alkynes have been studied using density functional theory. B3LYP/6-31G(d)/LANL2DZ optimized structures were further evaluated with the M06 functional, 6-311+G(2d,p) and LANL2DZ basis sets, and the SMD solvent model. The favored mechanism involves an initial ene-yne oxidative cyclization to form a ruthenacyclopentene intermediate. This mechanism is different from that found earlier with rhodium catalysts. The subsequent β-hydride elimination and cyclopropane cleavage are competitive, determining the experimental selectivity. In trans-VCP, the cyclopropane cleavage is intrinsically favored and leads to the (5+2) cycloaddition product. Although the same intrinsic preferences occur with the cis-VCP, an unfavorable rotation is required in order to generate the cis-double bond in seven-membered ring product, which reverses the selectivity. Acetone solvent is found to facilitate the acetonitrile dissociation from the precatalyst, destabilizing the resting state of the catalyst and leading to a lower overall reaction barrier. In addition, the origins of diastereoselectivities when the allylic hydroxyl group is trans to the bridgehead hydrogen are found to be the electrostatic interactions. In the pathway that generates the favored diastereomer, the oxygen lone pairs from the substituent are closer to the cationic catalyst center and provide stabilizing electrostatic interactions. Similar pathways also determine the regioselectivities, that is, whether the more or less substituted C-C bond of cyclopropane is cleaved. In the trans-1,2-disubstitued cyclopropane substrate, the substituent from the cyclopropane is away from the reaction center in both pathways, and low regioselectivity is found. In contrast, the cleavage of the more substituted C-C bond of the cis-1,2-disubstituted cyclopropane has steric repulsions from the substituent, and thus higher regioselectivity is found.

Enhanced chemical reactions of oxygen at grain boundaries in polycrystalline graphene

Oxygen adatoms on graphene and their potential reactions have been studied extensively as a way to modify and control the material’s properties. Here, we report first-principles calculations and Kinetic Monte Carlo simulations to describe oxygen binding, diffusion, and reactions on graphene in the presence of grain boundaries. We show that the defects attract and accumulate oxygen caused by the local strain. Moreover, we find that the reaction of a three-atom oxygen cluster, which consumes carbon atoms and creates vacancies in graphene, has a lower reaction barrier at grain boundaries than that on pristine graphene. Kinetic Monte Carlo simulations suggest that the dynamics of oxygen on graphene is controlled by two processes, oxygen reaction and migration, which depend on temperature and oxygen coverage. Because of the comparable activation barrier for both processes, etching at grain boundaries and the pristine region occurs simultaneously.

Comparison of Cu‐ZSM‐5 Zeolites and Cu‐MOF‐505 Metal‐Organic Frameworks as Heterogeneous Catalysts for the Mukaiyama Aldol Reaction: A DFT Mechanistic Study

The density functional theory (DFT) model ONIOM(M06L/6-311++G(2df,2p):UFF was employed to reveal the catalytic activity of Cu(II) in the paddle-wheel unit of the metal-organic framework (MOF)-505 material in the Mukaiyama aldol reaction compared with the activity of Cu-ZSM-5 zeolites. The aldol reaction between a silyl enol ether and formaldehyde catalyzed by the Lewis acidic site of both materials takes place through a concerted pathway, in which the formation of the CC bond and the transfer of the silyl group occurs in a single step. MOF-505 and Cu-ZSM-5 are predicted to be efficient catalysts for this reaction as they strongly activate the formaldehyde carbonyl carbon electrophile, which leads to a considerably lower reaction barrier compared with the gas-phase system. Both MOF-505 and Cu-ZSM-5 catalysts stabilize the reacting species along the reaction coordinate, thereby lowering the activation energy, compared to the gas-phase system. The activation barriers for the MOF-505, Cu-ZSM-5, and gas-phase system are 48, 21, and 61 kJ mol(-1) , respectively. Our results show the importance of the enveloping framework by stabilizing the reacting species and promoting the reaction.

Computational Mechanistic Study of Borohydride Electrochemical Oxidation on Au3Ni(111)

Au-3d metal alloys have recently gained interest for use as anode catalysts for direct borohydride fuel cells since these are less expensive than pure Au and exhibit desirable properties for borohydride oxidation. In this paper, a mechanistic study on the electrochemical oxidation of borohydride on Au3Ni(111) using first principles calculations based on spin-polarized density functional theory is presented. A reaction energy diagram showing the free energies of possible elementary surface-bound species on Au3Ni(111) as a function of electrode potential is constructed to show the favorable reaction path for a complete eight-electron oxidation of borohydride. As compared to pure Au, the adsorption of borohydride is favorable on Au3Ni(111) at lower potential due to the greater stability of borohydride on this surface, which is attributed to the upshift of the derived antibonding states of the BH4-sp and Au3Ni-d interaction with respect to pure Au. At a potential of −0.44 V vs NHE and T = 300 K, all subsequent elementary reaction steps for the complete oxidation of borohydride are downhill in energy with B(OH)3,ads as the highly favored final adsorbed species. The overall oxidation is limited by the initial adsorption of borohydride on the surface since it requires the highest electrode potential requirement among all electrochemical steps considered. Calculation of the dehydrogenation barrier of borohydride provides significant evidence that a more favorable elementary reaction on Au3Ni(111) as compared to Au(111) also leads to a lower reaction barrier.

Free radical routes for prebiotic formation of DNA nucleobases from formamide

Modeling the complicated chemical reactions in the interstellar medium and surface materials of Titan is nontrivial. Since both the atmosphere and the surface are rich in organic molecules, the chemistry may have important implications for the origin of biomolecules. Prebiotic synthesis of DNA nucleobases from simple molecules such as formamide has been known for more than half a century. In this study, new free radical pathways leading to the synthesis of guanine, hypoxanthine, purine, and adenine have been studied using density functional theory (B3LYP with the 6-311G(d,p) basis set). The pathways of the selected nucleobases demonstrate the importance of free radicals in the production of useful biomolecules under conditions appropriate for the interstellar medium or on Titan. The pathways may be universal in nature and proceed without solvent requirements. Calculations indicate that radical pathways yield lower reaction barriers as compared to previously reported pathways. Overall, these results suggest that the chemistry on Titan's surface and/or the growth of organic particulates in the haze layers in Titan's atmosphere likely involve free radicals. The mechanisms demonstrate that important prebiotic precursors can be predicted. The reaction sequences reported here may lead to the production and build-up of molecules with prebiotic relevance.

Efficient hydrogenation over single-site bimetallic RuSn clusters

Hydrogenation of ethene to ethane over single-site RuN and (RuSn)N clusters is investigated using Density Functional Theory calculations. The critical transition state barrier, namely the last hydrogenation step, correlates linearly for RuN with the adsorption energies of the reactants. Addition of Sn to the Ru-clusters breaks this relation and allows for lower reaction barriers. In general, Sn is found to have pronounced effects on the geometrical and electronic properties of RuN clusters with N≤ 12. RuN clusters preferably adopt cubic conformations with high spin states, whereas (RuSn)N have low spin states and form compact Ru cores capped with Sn atoms.

Density Functional Theory Study of Methane Oxidation and Reforming on Pt(111) and Pt(211)

The activation barriers of elementary-like reactions pertaining to the oxidation and reforming of methane on Pt(111) and Pt(211) surfaces have been calculated using periodic density functional theory (DFT) calculations. We have investigated the adsorption of CHx(x=1–3)OH and CHx(x=1–3)O, all the O and OH-assisted dehydrogenation reactions of CHx(x=1–4), all the C–O bond coupling reactions forming C1 oxygenates, and their subsequent dehydrogenation. It has been found that (i) COH and CHO are the most stable C1 oxygenates on Pt(111) and Pt(211), repectively; (ii) In the presence of O on Pt(211), oxidative dehydrogenation of CH by O is more kinetically favorable than the pyrolytic CH dehydrogenation; (iii) CO can be generated by oxidation of C with a low reaction barrier on Pt(211); (iv) The reactions involving OH and the dehydrogenation of CHx(x=1–3)OH and CHx(x=1–3)O appear to be secondary reaction pathways on Pt. Based on the activation barriers, we conclude that the major reaction pathways on Pt(111) and...

Sequential adjacent Si dimer dechlorination mechanism of perchloroethylene adsorption on Si(1 0 0) with temperature evolution

To elucidate the peak shifting of C-1s in X-ray photoelectron spectrum (XPS) of perchloroethylene (PCE) adsorption on Si(100), the sequential adjacent Si dimer dechlorination mechanism was proposed based on first principles calculations. The highly-symmetric Cl atoms of PCE induce three possible initial di-dechlorination processes occurring on intra, inter-dimer and iso intra-dimer, respectively, to yield three tetra-σ states. These tetra-σ states are identified to coexist at room temperature (RT) due to the relatively low reaction barriers (<0.59eV). However, their further di-dechlorination to form intra and inter-dimer hexa-σ states requires much higher activation barriers (>1.08eV), which leads to hexa-σ states only exist at elevated temperatures although they are found to be the most stable in terms of energetics. The calculated ionization energies (IEs) of C-1s core electron and vibrational frequencies of various potential adspecies are well consistent with the experimental data observed by XPS and vibrational electron energy loss spectroscopy (EELS), which further corroborates the sequential dechlorination processes of PCE on Si(100).

Pivotal Role of Water in Terminating Enzymatic Function: A Density Functional Theory Study of the Mechanism-Based Inactivation of Cytochromes P450

The importance of the mechanism-based inactivation (MBI) of enzymes, which has a variety of physiological effects and therapeutic implications, has been garnering appreciation. Density functional theory calculations were undertaken to gain a clear understanding of the MBI of a cytochrome P450 enzyme (CYP2B4) by tert-butylphenylacetylene (tBPA). The results of calculations suggest that, in accordance with previous proposals, the reaction proceeds via a ketene-type metabolic intermediate. Once an oxoiron(IV) porphyryn π-cation radical intermediate (compound I) of P450 is generated at the heme reaction site, ketene formation is facile, as the terminal acetylene of tBPA can form a C-O bond with the oxo unit of compound I with a relatively low reaction barrier (14.1 kcal/mol). Unexpectedly, it was found that the ketene-type intermediate was not very reactive. Its reaction with the hydroxyl group of a threonine (Thr302) to form an ester bond required a substantial barrier (38.2 kcal/mol). The high barrier disfavored the mechanism by which these species react directly. However, the introduction of a water molecule in the reaction center led to its active participation in the reaction. The water was capable of donating its proton to the tBPA molecule, while accepting the proton of threonine. This water-mediated mechanism lowered the reaction barrier for the formation of an ester bond by about 20 kcal/mol. Therefore, our study suggests that a water molecule, which can easily gain access to the threonine residue through the proton-relay channel, plays a critical role in enhancing the covalent modification of threonine by terminal acetylene compounds. Another type of MBI by acetylenes, N-alkylation of the heme prosthetic group, was less favorable than the threonine modification pathway.