On the Reaction of Glycerol Dehydratase with But‐3‐ene‐1,2‐diol

Intriguing inactivation : Calculations suggest that the ability of relatively high‐energy radical intermediates to inactivate glycerol dehydratase (GDH) may reflect a general and hitherto unidentified inactivation mechanism in the reaction of coenzyme B₁₂‐dependent enzymes and 3‐unsaturated 1,2‐diols (see scheme; AdoCbl: adenosylcobalamin or coenzyme B₁₂).

     

The Stability of α‐Hydroperoxyalkyl Radicals

High‐level ab initio and Born–Oppenheimer molecular dynamic calculations have been carried out on a series of hydroperoxyalkyl (α‐QOOH) radicals with the aim of investigating the stability and unimolecular decomposition mechanism into QO+OH of these species. Dissociation was shown to take place through rotation of the C?O(OH) bond rather than through elongation of the CO?OH bond. Through the C?O(OH) rotation, the unpaired electron of the radical overlaps with the electron density on the O?OH bond, and from this overlap the C=O π bond forms and the O?OH bond breaks spontaneously. The CH₂OOH, CH(CH₃)OOH, CH(OH)OOH, and α‐hydroperoxycycloheptadienyl radical were found to decompose spontaneously, but the CH(CHO)OOH has a decomposition energy barrier of 5.95 kcal mol^?1 owing to its steric and electronic features. The systems studied in this work provide the first insights into how structural and electronic effects govern the stabilizing influence on elusive α‐QOOH radicals.     

Ab initio static and molecular dynamics study of 4-styrylpyridine.

We report an in‐depth theoretical study of 4‐styrylpyridine in its singlet S₀ ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree–Fock (HF), second‐order Møller–Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post‐HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis?trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car–Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within ≈1 ps during the simulation carried out at 150 K on this isomer.     

DFT Methods to Study the Reaction Mechanism of Iridium‐Catalyzed Hydrogenation of Olefins: Which Functional Should be Chosen?

To enable the selection of more accurate computational methods for the future theoretical exploration of the reaction mechanism of Ir‐catalyzed olefin hydrogenation, we compared high‐level ab initio coupled cluster and DFT calculations with a simplified model of Pfaltz's Ir/P,N‐type catalyst for all four previously proposed Ir^I/Ir^III and Ir^III/Ir^V mechanisms. Through the systematic assessment of the DFT performances, the DFT empirical dispersion correction (DFT‐D3) is found to be indispensable for improving the accuracy of relative energies between the Ir^I/Ir^III and Ir^III/Ir^V mechanisms. After including the DFT‐D3 correction, the three best performing density functionals (DFs) are B2‐PLYP, BP86, and TPSSh. In these recommended DFs, the computationally more expensive double‐hybrid functional B2‐PLYP‐D3 has a balanced and outstanding performance for calculations of the reaction barriers, reaction energies, and energy gaps between different mechanisms, whereas the less costly BP86‐D3 and TPSSh‐D3 methods have outstanding, but relatively less uniform performances.     

Berry pseudorotation mechanism for the interpretation of the 19F NMR spectrum in PF5 by ab initio molecular dynamics simulations.

For the first time, theoretical evidence that confirms the importance of the Berry pseudorotation process in the interpretation of the 19F NMR spectrum of phosphorus pentafluoride (PF5) is presented. Ab initio molecular dynamics simulations have been performed to generate a large number of configurations used for NMR parameter computations at the density functional theory level. Two different temperatures were set to highlight the effect of pseudorotation process on the NMR spectrum. Average 19F chemical shifts and spin-spin coupling constants calculated for the five fluorine atoms converge towards the NMR equivalence of the five atoms when the Berry pseudorotation mechanism is accounted for.     

Understanding the Role of Water in Aqueous Ruthenium‐Catalyzed Transfer Hydrogenation of Ketones.

We report an accurate computational study of the role of water in transfer hydrogenation of formaldehyde with a ruthenium‐based catalyst using a water‐specific model. Our results suggest that the reaction mechanism in aqueous solution is significantly different from that in the gas phase or in methanol solution. Previous theoretical studies have shown a concerted hydride and proton transfer in the gas phase (M. Yamakawa, H. Ito, R. Noyori, J. Am. Chem. Soc. 2000 , 122, 1466–1478;J.‐W. Handgraaf, J. N. H. Reek, E. J. Meijer, Organometallics 2003 , 22, 3150–3157; D. A. Alonso, P. Brandt, S. J. M. Nordin, P. G. Andersson, J. Am. Chem. Soc. 1999 , 121, 9580–9588; D. G. I. Petra, J. N. H. Reek, J.‐W. Handgraaf, E. J. Meijer, P. Dierkes, P. C. J. Kamer, J. Brussee, H. E. Schoemaker, P. W. N. M. van Leeuwen, Chem. Eur. J. 2000 , 6, 2818–2829), whereas a delayed, solvent‐mediated proton transfer has been observed in methanol solution (J.‐W. Handgraaf, E. J. Meijer, J. Am. Chem. Soc. 2007 , 129, 3099–3103). In aqueous solution, a concerted transition state is observed, as in the previous studies. However, only the hydride is transferred at that point, whereas the proton is transferred later by a water molecule instead of the catalyst.     

Computational studies on azaphosphiridines, or how to effect ring-opening processes through selective bond activation

The relative energies of azaphosphiridine and its isomers, the ring stability towards valence isomerization, and the ring strain, as well as the kinetics and thermodynamics of possible ring‐opening reactions of P^III derivatives ( 1 – 5 ) and P^V chalcogenides ( 6 – 9 ; O to Te), were studied at high levels of theory (up to CCSD(T)). The barrier to inversion at the nitrogen atom in the trimethyl‐substituted P^III derivative 5 increases from 12.11 to 15.25 kcal mol^?1 in the P‐oxide derivative 6 (P^V); the relatively high barrier to inversion at the phosphorus in 5 (75.38 kcal mol^?1) points to a configurationally stable center (MP2/def2‐TZVPP//BP86/def2‐TZVP). The ring strain for azaphosphiridine 5 (av. 22.6 kcal mol^?1) was found to increase upon P‐oxidation ( 6 ) (30.8 kcal mol^?1; same level of theory). Various ring‐bond‐activation processes were studied: N‐protonation of P^III ( 5 ) and P^V ( 6 , 7 ) derivatives leads to highly activated species that readily undergo P? N bond cleavage. In contrast, metal chlorides such as LiCl, CuCl, CuCl₂, BeCl₂, BCl₃, AlCl₃, TiCl₃, and TiCl₄ show little P? N bond activation in 5 and 7 . Remarkably, TiCl₃ selectively activates the C? N bond, and induces stronger bond activation for P^V ( 6, 7 ) than for P^III azaphosphiridines ( 5 ). The ring‐expanding rearrangement of P^V azaphosphiridines 6 – 9 to yield P^III 1,3,2‐chalcogena‐azaphosphetidines 32 a – d is predicted to be preferred for the heavier chalcogenides 7 – 9 , but not for the P‐oxide 6 . The first comparative analysis of three bond strength parameters is presented: 1) the electron density at bond critical points, 2) Wiberg’s bond index, and 3) the relaxed force constant. This reveals the usefulness of these parameters in assessing the degree of ring bond activation.     

A Computational Study on Closed-Shell Molecular Hexafluorides MF6 (M=S,Se, Te,Po, Xe,Rn, Cr,Mo, W,U) – Molecular Structure,Anharmonic Frequency Calculations,and Prediction of the NdF6 Molecule

Quantum chemical methods were used to study the molecular structure and anharmonic IR spectra of the experimentally known closed-shell molecular hexafluorides MF₆ (M=S, Se, Te, Xe, Mo, W, U). First, the molecular structures and harmonic frequencies were investigated using Density Functional Theory (DFT) with all-electron basis sets and explicitly considering the influence of spin-orbit coupling. Second, anharmonic frequencies and IR intensities were calculated with the CCSD(T) coupled cluster method and compared, where available, with IR spectra recorded by us. These comparisons showed satisfactory results. The anharmonic IR spectra provide means for identifying experimentally too little studied or unknown MF₆ molecules with M=Cr, Po, Rn. To the best of our knowledge, we predict the NdF₆ molecule for the first time and show it to be a true local minimum on the potential energy surface. We used intrinsic bond orbital (IBO) analyses to characterize the bonding situation in comparison with the UF₆ molecule.     

Accurate pKa Calculation of the Conjugate Acids of Alkanolamines,Alkaloids and Nucleotide Bases by Quantum Chemical Methods

The pK_a of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08‐HX and M11‐L) and ab initio methods (SCS‐MP2, G3). Implicit solvent effects are included with a conductor‐like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS‐MP2 and M11‐L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pK_a units, in all cases. Extending this method to the pK_a calculation of 35 nitrogen‐containing compounds spanning 12 pK_a units showed an excellent correlation between experimental and computational pK_a values of these 35 amines with the computationally low‐cost SM8/M11‐L density functional approach.     

CHF_2CF_2CH_2OCHF_2与OH自由基反应机理的理论研究

采用从头算和密度泛函方法研究了多通道反应CHF2CF2CH2OCHF2+OH→产物的反应机理.首先在BMK/6-311+G(d,p)水平下优化了稳定点的几何构型并计算了振动频率;然后在BMC-CCSD水平下,对势能面进行高水平能量校正.结果表明,此反应存在提氢和取代两类反应通道,但是无论从动力学还是从热力学分析,提氢反应通道才是主要的反应通道,且从-CH2-基团上提取氢原子的提氢通道是主要的反应通道.