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Chan B, O’Reilly RJ, Easton CJ, Radom L. Reactivities of Amino Acid Derivatives Toward Hydrogen Abstraction by Cl• and OH•. J Org Chem 2012; 77:9807-12. [DOI: 10.1021/jo3021538] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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52
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Menon AS, Bally T, Radom L. Influence of Connector Groups on the Interactions of Substituents with Carbon-Centered Radicals. J Phys Chem A 2012; 116:10203-8. [DOI: 10.1021/jp3064245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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53
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Chan B, Gill PMW, Radom L. Performance of Gradient-Corrected and Hybrid Density Functional Theory: Role of the Underlying Local Density Approximation and the Gradient Correction. J Chem Theory Comput 2012; 8:4899-906. [DOI: 10.1021/ct300603d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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54
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Chan B, Radom L. W1X-1 and W1X-2: W1-Quality Accuracy with an Order of Magnitude Reduction in Computational Cost. J Chem Theory Comput 2012; 8:4259-69. [DOI: 10.1021/ct300632p] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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55
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Chan B, Trevitt AJ, Blanksby SJ, Radom L. Comment on the Ionization Energy of B2F4. J Phys Chem A 2012; 116:9214-5. [DOI: 10.1021/jp306150u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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56
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Chan B, Karton A, Raghavachari K, Radom L. Heats of Formation for CrO, CrO2, and CrO3: An Extreme Challenge for Black-Box Composite Procedures. J Chem Theory Comput 2012; 8:3159-66. [DOI: 10.1021/ct300495m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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57
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Karton A, O’Reilly RJ, Chan B, Radom L. Determination of Barrier Heights for Proton Exchange in Small Water, Ammonia, and Hydrogen Fluoride Clusters with G4(MP2)-Type, MPn, and SCS-MPn Procedures—A Caveat. J Chem Theory Comput 2012; 8:3128-36. [DOI: 10.1021/ct3004723] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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58
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Chan B, Radom L. BDE261: a comprehensive set of high-level theoretical bond dissociation enthalpies. J Phys Chem A 2012; 116:4975-86. [PMID: 22587308 DOI: 10.1021/jp302542z] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have used the high-level W1w protocol to compile a comprehensive collection of 261 bond dissociation enthalpies (BDEs) for bonds connecting hydrogen, first-row and second-row p-block elements. Together they cover 45 bond types, and we term this the BDE261 set. We have used these benchmark values to assess the performance of computationally less demanding theoretical procedures, including density functional theory (DFT), double-hybrid DFT (DHDFT), and high-level composite procedures. We find that the M06-2X (DFT), ROB2-PLYP and DuT-D3 (DHDFT), and G3X(MP2)-RAD and G4(MP2)-6X (composite) procedures yield absolute BDEs with satisfactory to excellent accuracy. Overall, we recommend G4(MP2)-6X as an accurate and relatively cost-effective procedure for the direct computation of BDEs. One important finding is that the deviations for DFT and (especially) DHDFT procedures are often quite systematic. This allows an alternative approach to obtaining accurate absolute BDEs, namely, to evaluate accurate relative BDEs (RBDEs) using a computationally less demanding procedure, and to use these RBDEs in combination with appropriate and accurate reference BDEs to give accurate absolute BDEs. We recommend DuT-D3 for this purpose. For a still less computationally demanding approach, we introduce the deviation from additivity of the RBDE (DARBDE), and demonstrate that the combination of lower-level DARBDEs for larger systems and higher-level (W1w) reference RBDEs and BDEs for small systems can be utilized to obtain improved RBDEs for multiply substituted systems at low cost.
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Karton A, O’Reilly RJ, Radom L. Assessment of Theoretical Procedures for Calculating Barrier Heights for a Diverse Set of Water-Catalyzed Proton-Transfer Reactions. J Phys Chem A 2012; 116:4211-21. [DOI: 10.1021/jp301499y] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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60
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Chan B, Radom L. Approaches for Obtaining Accurate Rate Constants for Hydrogen Abstraction by a Chlorine Atom. J Phys Chem A 2012; 116:3745-52. [PMID: 22468903 DOI: 10.1021/jp3007409] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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61
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Bucher D, Sandala GM, Durbeej B, Radom L, Smith DM. The Elusive 5′-Deoxyadenosyl Radical in Coenzyme-B12-Mediated Reactions. J Am Chem Soc 2012; 134:1591-9. [DOI: 10.1021/ja207809b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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62
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Chalyavi N, Bacskay GB, Menon AS, Troy TP, Davis NJLK, Radom L, Reid SA, Schmidt TW. Spectroscopy and thermochemistry of a jet-cooled open-shell polyene: 1,4-pentadienyl radical. J Chem Phys 2011; 135:124306. [DOI: 10.1063/1.3640475] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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63
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O'Reilly RJ, Chan B, Taylor MS, Ivanic S, Bacskay GB, Easton CJ, Radom L. Hydrogen abstraction by chlorine atom from amino acids: remarkable influence of polar effects on regioselectivity. J Am Chem Soc 2011; 133:16553-9. [PMID: 21942745 DOI: 10.1021/ja205962b] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Quantum chemistry computations have been used to investigate hydrogen-atom abstraction by chlorine atom from protonated and N-acetylated amino acids. The results are consistent with the decreased reactivity at the backbone α-carbon and adjacent side-chain positions that is observed experimentally. The individual effects of NH(3)(+), COOH, and NHAc substituents have been examined and reveal important insights. The NH(3)(+) group in isolation is found to be deactivating at the α-position, while the acetamido group is activating. For the COOH group, polar effects lead to a contrathermodynamic deactivation of the thermodynamically most favorable α-abstraction. In the N-acetylamino acid, the α-position is deactivated by the combined inductive effect of the substituents and the presence of an early transition structure, again overriding the greater thermodynamic stability of the α-centered radical product. Deactivation of the α-, β-, and γ-positions results in a peculiar stability for amino acids and peptides and their derivatives with respect to radical degradation.
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Chan B, Radom L. Obtaining Good Performance With Triple-ζ-Type Basis Sets in Double-Hybrid Density Functional Theory Procedures. J Chem Theory Comput 2011; 7:2852-63. [PMID: 26605476 DOI: 10.1021/ct200396x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A variety of combinations of B-LYP-based double-hybrid density functional theory (DHDFT) procedures and basis sets have been examined. A general observation is that the optimal combination of exchange contributions is in the proximity of 30% Becke 1988 (B88) exchange and 70% Hartree-Fock (HF) exchange, while for the correlation contributions, the use of independently optimized spin-component-scaled Møller-Plesset second-order perturbation theory (SCS-MP2) parameters (MP2OS and MP2SS) is beneficial. The triple-ζ Dunning aug'-cc-pVTZ+d and Pople 6-311+G(3df,2p)+d basis sets are found to be cost-effective for DHDFT methods. As a result, we have formulated the DuT-D3 DHDFT procedure, which employs the aug'-cc-pVTZ+d basis set and includes 30% B88 and 70% HF exchange energies, 59% LYP, 47% MP2OS, and 36% MP2SS correlation energies, and a D3 dispersion correction with the parameters s6 = 0.5, sr,6 = 1.569, and s8 = 0.35. Likewise, the PoT-D3 DHDFT procedure was formulated with the 6-311+G(3df,2p)+d basis set and has 32% B88 and 68% HF exchange energies, 63% LYP, 46% MP2OS, and 27% MP2SS correlation energies, and the D3 parameters s6 = 0.5, sr,6 = 1.569, and s8 = 0.30. Testing using the large E3 set of 740 energies demonstrates the robustness of these methods. Further comparisons show that the performance of these methods, particularly DuT-D3, compares favorably with the previously reported DSD-B-LYP and DSD-B-LYP-D3 methods used in conjunction with quadruple-ζ aug'-pc3+d and aug'-def2-QZVP basis sets but at lower computational expense. The previously reported ωB97X-(LP)/6-311++G(3df,3pd) procedure also performs very well. Our findings highlight the cost-effectiveness of appropriate- and moderate-sized triple-ζ basis sets in the application of DHDFT procedures.
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65
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Chan B, Radom L. Assessment of theoretical procedures for hydrogen-atom abstraction by chlorine, and related reactions. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0967-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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66
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Nagy P, Karton A, Betz A, Peskin AV, Pace P, O'Reilly RJ, Hampton MB, Radom L, Winterbourn CC. Model for the exceptional reactivity of peroxiredoxins 2 and 3 with hydrogen peroxide: a kinetic and computational study. J Biol Chem 2011; 286:18048-55. [PMID: 21385867 PMCID: PMC3093878 DOI: 10.1074/jbc.m111.232355] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 03/02/2011] [Indexed: 12/30/2022] Open
Abstract
Peroxiredoxins (Prx) are thiol peroxidases that exhibit exceptionally high reactivity toward peroxides, but the chemical basis for this is not well understood. We present strong experimental evidence that two highly conserved arginine residues play a vital role in this activity of human Prx2 and Prx3. Point mutation of either ArgI or ArgII (in Prx3 Arg-123 and Arg-146, which are ∼3-4 Å or ∼6-7 Å away from the active site peroxidative cysteine (C(p)), respectively) in each case resulted in a 5 orders of magnitude loss in reactivity. A further 2 orders of magnitude decrease in the second-order rate constant was observed for the double arginine mutants of both isoforms, suggesting a cooperative function for these residues. Detailed ab initio theoretical calculations carried out with the high level G4 procedure suggest strong catalytic effects of H-bond-donating functional groups to the C(p) sulfur and the reactive and leaving oxygens of the peroxide in a cooperative manner. Using a guanidinium cation in the calculations to mimic the functional group of arginine, we were able to locate two transition structures that indicate rate enhancements consistent with our experimentally observed rate constants. Our results provide strong evidence for a vital role of ArgI in activating the peroxide that also involves H-bonding to ArgII. This mechanism could explain the exceptional reactivity of peroxiredoxins toward H(2)O(2) and may have wider implications for protein thiol reactivity toward peroxides.
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67
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O’Reilly RJ, Karton A, Radom L. Effect of Substituents on the Strength of N–X (X = H, F, and Cl) Bond Dissociation Energies: A High-Level Quantum Chemical Study. J Phys Chem A 2011; 115:5496-504. [DOI: 10.1021/jp203108e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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68
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Pattison DI, O'Reilly RJ, Skaff O, Radom L, Anderson RF, Davies MJ. One-electron reduction of N-chlorinated and N-brominated species is a source of radicals and bromine atom formation. Chem Res Toxicol 2011; 24:371-82. [PMID: 21344936 DOI: 10.1021/tx100325z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hypochlorous (HOCl) and hypobromous (HOBr) acids are strong bactericidal oxidants that are generated by the human immune system but are implicated in the development of many human inflammatory diseases (e.g., atherosclerosis, asthma). These oxidants react readily with sulfur- and nitrogen-containing nucleophiles, with the latter generating N-halogenated species (e.g., chloramines/bromamines (RR'NX; X = Cl, Br)) as initial products. Redox-active metal ions and superoxide radicals (O(2)(•-)) can reduce N-halogenated species to nitrogen- and carbon-centered radicals. N-Halogenated species and O(2)(•-) are generated simultaneously at sites of inflammation, but the significance of their interactions remains unclear. In the present study, rate constants for the reduction of N-halogenated amines, amides, and imides to model potential biological substrates have been determined. Hydrated electrons reduce these species with k(2) > 10(9) M(-1) s(-1), whereas O(2)(•-) reduced only N-halogenated imides with complex kinetics indicative of chain reactions. For N-bromoimides, heterolytic cleavage of the N-Br bond yielded bromine atoms (Br(•)), whereas for other substrates, N-centered radicals and Cl(-)/Br(-) were produced. High-level quantum chemical procedures have been used to calculate gas-phase electron affinities and aqueous solution reduction potentials. The effects of substituents on the electron affinities of aminyl, amidyl, and imidyl radicals are rationalized on the basis of differential effects on the stabilities of the radicals and anions. The calculated reduction potentials are consistent with the experimental observations, with Br(•) production predicted for N-bromosuccinimide, while halide ion formation is predicted in all other cases. These data suggest that interaction of N-halogenated species with O(2)(•-) may produce deleterious N-centered radicals and Br(•).
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69
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Menon AS, Henry DJ, Bally T, Radom L. Effect of substituents on the stabilities of multiply-substituted carbon-centered radicals. Org Biomol Chem 2011; 9:3636-57. [DOI: 10.1039/c1ob05196b] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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70
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Abstract
High-level composite, ab initio and density functional theory (DFT) procedures have been employed to study O–H bond dissociation energies (BDEs), as well as radical stabilization energies (RSEs) in the oxygen-centred radicals that are formed in the dissociation of the O–H bonds. Benchmark values are provided by Wn results up to W3.2 and W4.x. We are able to recommend revised BDE values for FO–H (415.6 ± 3 kJ mol–1), MeC(O)O–H (459.8 ± 6 kJ mol–1) and CF3CH2O–H (461.9 ± 6 kJ mol–1) on the basis of high-level calculations. We find that Gn-type procedures are generally reliable and cost-effective, and that some contemporary functionals and double-hybrid DFT procedures also provide adequate O–H BDEs/RSEs. We note that the variations in the O–H BDEs are associated with variations in the stabilities of not only the radicals but also the closed-shell precursor molecules. Most substituents destabilize both species, with σ-electron-withdrawing groups having larger destabilizing effects, while π-electron acceptors are stabilizing. Although there is little correlation between the stabilizing/destabilizing effects of the substituents and the RSEs, we present some general patterns in the RSEs that emerge from the present study.
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71
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Troy TP, Chalyavi N, Menon AS, O'Connor GD, Fückel B, Nauta K, Radom L, Schmidt TW. The spectroscopy and thermochemistry of phenylallyl radical chromophores. Chem Sci 2011. [DOI: 10.1039/c1sc00247c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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72
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Chan B, Deng J, Radom L. G4(MP2)-6X: A Cost-Effective Improvement to G4(MP2). J Chem Theory Comput 2010; 7:112-20. [DOI: 10.1021/ct100542x] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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73
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Chan B, Del Bene JE, Radom L. What factors determine whether a proton-bound homodimer has a symmetric or an asymmetric hydrogen bond? Mol Phys 2010. [DOI: 10.1080/00268970902740571] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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74
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Chan B, Coote ML, Radom L. G4-SP, G4(MP2)-SP, G4-sc, and G4(MP2)-sc: Modifications to G4 and G4(MP2) for the Treatment of Medium-Sized Radicals. J Chem Theory Comput 2010; 6:2647-53. [DOI: 10.1021/ct100266u] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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75
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Chan B, Radom L. A computational study of methanol-to-hydrocarbon conversion — Towards the design of a low-barrier process. CAN J CHEM 2010. [DOI: 10.1139/v10-043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Computational quantum chemistry has been employed to examine the production of ethylene with methanol-to-hydrocarbon (MTH) processes via a carbon pool mechanism. We find that the M05-2X functional performs well for the types of reactions that are involved. The methylation reactions of the aromatic cocatalyst are the most energy-demanding steps in the process. For the subsequent production of C2H4, we have identified a low-energy pathway that involves multiple methyl shifts, followed by concerted deprotonation and C2H4 elimination. The substitutions of the Al and Si atoms in the participating Si–OH–Al moiety of zeolite catalysts with Ga and Ge do not lead to lower barriers for the methylation reactions, nor does the use of a more electron-rich aromatic cocatalyst. However, we find that the use of two cocatalysts, a nucleophile and an aromatic carbon pool, can provide an overall low-energy pathway for the MTH process.
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