Ab initio study of β-lactam antibiotics. II. Potential energy surface for the amidic CN bond breaking in the 3-cephem + OH− reaction and comparison with the β-lactam + OH− reaction

The potential energy surface for the β-lactam amidic CN bond breaking in the 3-cephem + OH^? reaction was investigated by using the ab initio Hartree—Fock method with a 9s6p/7s3p/3s basis set. The investigated reaction is a model of the reaction between an antibiotic cephalosporin and an enzymatic nucleophilic group, this last reaction being related to the mode of action of β-lactam antibiotics. The minimum-energy reaction path is characterized by a tetrahedral intermediate ≈ 116 kcal mol^?1 more stable than the reagents, by a barrier which corresponds to the partial breaking of the amidic bond and is ≈ 7 kcal mol^?1 above the intermediate and by a product ≈ 31 kcal mol^?1 more stable than the intermediate. The analysis of the wavefunction along the reaction path and the comparison with the β-lactam + OH^? reaction pointed out the role of electron-withdrawing groups on the height of the barrier and the role of intramolecular hydrogen bonds on the structure and energy of the product. The calculations suggest a model of the antibiotic activity of cephalosporins which is compared with previous qualitative pictures.     

C-H bond activation of methane in aqueous solution: a hybrid quantum mechanical/effective fragment potential study

In this study, we investigated the C? H bond activation of methane catalyzed by the complex [PtCl₄]^2?, using the hybrid quantum mechanical/effective fragment potential (EFP) approach. We analyzed the structures, energetic properties, and reaction mechanism involved in the elementary steps that compose the catalytic cycle of the Shilov reaction. Our B3LYP/SBKJC/cc‐pVDZ/EFP results show that the methane activation may proceed through two pathways: (i) electrophilic addition or (ii) direct oxidative addition of the C? H bond of the alkane. The electrophilic addition pathway proceeds in two steps with formation of a σ‐methane complex, with a Gibbs free energy barrier of 24.6 kcal mol^?1, followed by the cleavage of the C? H bond, with an energy barrier of 4.3 kcal mol^?1. The activation Gibbs free energy, calculated for the methane uptake step was 24.6 kcal mol^?1, which is in good agreement with experimental value of 23.1 kcal mol^?1 obtained for a related system. The results shows that the activation of the C? H bond promoted by the [PtCl₄]^2? catalyst in aqueous solution occurs through a direct oxidative addition of the C? H bond, in a single step, with an activation free energy of 25.2 kcal mol^?1, as the electrophilic addition pathway leads to the formation of a σ‐methane intermediate that rapidly undergoes decomposition. The inclusion of long‐range solvent effects with polarizable continuum model does not change the activation energies computed at the B3LYP/SBKJC/cc‐pVDZ/EFP level of theory significantly, indicating that the large EFP water cluster used, obtained from Monte Carlo simulations and analysis of the center‐of‐mass radial pair distribution function, captures the most important solvent effects. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Mechanism of nucleophilic fluorination promoted by bis‐tert‐alcohol‐functionalized crown‐6‐calix[4]arene

Theoretical calculations were performed to elucidate the ability of the recently reported bis‐tert‐alcohol‐functionalized crown‐6‐calix[4]arene (BACCA) molecule to promote nucleophilic fluorination of alkyl mesylates with cesium fluoride reagent. It was found that a similar structure, named BACCAt, can separate the cesium fluoride ion pair in tert‐butanol solution. This separation has a free energy cost, even considering the double hydrogen bonds with the fluoride ion. The solvent has an important effect on the stabilization of this complex, due to interaction with the high dipole moment of the separated ion pair. The observed rate acceleration effect involves a structure with double hydrogen bonds between the BACCAt and the centers of negative charges of the S_N2 transition state. The predicted free energy barrier of 27.3 kcal mol⁻¹ is in excellent agreement with the estimated experimental value of 26.2 kcal mol⁻¹.     

Assessing the Viability of the Methylsulfinyl Radical-Ozone Reaction

Although integral to remote marine atmospheric sulfur chemistry, the reaction between methylsulfinyl radical (CH₃SO) and ozone poses challenges to theoretical treatments. The lone theoretical study on this reaction reported an unphysically large barrier of 66 kcal mol⁻¹ for abstraction of an oxygen atom from O₃ by CH₃SO. Herein, we demonstrate that this result stems from improper use of MP2 with a single-reference, unrestricted Hartree-Fock (UHF) wavefunction. We characterized the potential energy surface using density functional theory (DFT), as well as multireference methodologies employing a complete active-space self-consistent field (CASSCF) reference. Our DFT PES shows, in contrast to previous work, that the reaction proceeds by forming an addition adduct [CH₃S(O₃)O] in a deep potential well of 37 kcal mol⁻¹. An O−O bond of this adduct dissociates via a flat, low barrier of 1 kcal mol⁻¹ to give CH₃SO₂+O₂. The multireference computations show that the initial addition of CH₃SO+O₃ is barrierless. These results provide a more physically intuitive and accurate picture of this reaction than the previous theoretical study. In addition, our results imply that the CH₃SO₂ formed in this reaction can readily decompose to give SO₂ as a major product, in alignment with the literature on CH₃SO reactions.     

Ab initio study of β-lactam antibiotics. I. Potential energy surface for the amidic CN bond breaking in the β-lactam + OH− reaction

The potential energy surface of the β-lactam + OH^? reaction, related to the mode of action of β-lactam antibiotics, was investigated using the ab initio Hartree—Fock method with the STO-3G basis set. Three possible reaction paths for the B_AC2 breaking of the amidic CN bond were obtained and discussed. The minimum-energy reaction path is characterized by the following processes: (1) the formation of a tetrahedral intermediate, ≈ 121 kcal mol^?1 more stable than the reagents; (2) a barrier, ≈ 15 kcal mol^?1 above the intermediate, which is mainly due to the partial breaking of the amidic bond; (3) the complete breaking of the amidic bond concerted with a proton transfer till the formation of the final product, ≈ 34 kcal mol^?1 more stable than the intermediate. The evolution of some molecular orbitals and of the electron population along the reaction path was also discussed.     

Iridicycle‐Catalysed Imine Reduction: An Experimental and Computational Study of the Mechanism

The mechanism of imine reduction by formic acid with a single‐site iridicycle catalyst has been investigated by density functional theory (DFT), NMR spectroscopy, and kinetic measurements. The NMR and kinetic studies suggest that the transfer hydrogenation is turnover‐limited by the hydride formation step. The calculations reveal that, amongst a number of possibilities, hydride formation from the iridicycle and formate probably proceeds by an ion‐pair mechanism, whereas the hydride transfer to the imino bond occurs in an outer‐sphere manner. In the gas phase, in the most favourable pathway, the activation energies in the hydride formation and transfer steps are 26–28 and 7–8 kcal mol^?1, respectively. Introducing one explicit methanol molecule into the modelling alters the energy barrier significantly, reducing the energies to around 18 and 2 kcal mol^?1 for the two steps, respectively. The DFT investigation further shows that methanol participates in the transition state of the turnover‐limiting hydride formation step by hydrogen‐bonding to the formate anion and thereby stabilising the ion pair.     

1H and 13C NMR studies of some aromatic dilactones (precursors of paracyclophanes)

Carbon-13 and proton NMR data of macrocyclic diaromatic dilactones are presented. The observed behaviour of the spectra as a function of temperature shows that the energy barrier for the re-orientation of the side chains is lower than 49 kJ mol^?1 (12 kcal mol^?1) and that the energy barrier for the rotation of the aromatic rings is larger than 99 kJ mol^?1 (24 kcal mol^?1). Hence, chiral substituted dilactones of this type will be resolvable, and the enantiomers can be easily handled at room temperature.     

Quantumchemical investigation of borabenzene adduct with pyridine

Atomic charges and structural parameters of borabenzene, pyridine and their adduct in free state, in liquid argon and in tetrahydrofuran are calculated by the quantum-chemical method B3LYP/6-311G(3d5f7,p) &; PCM. Mutual polarization of the adduct and medium results in small increase in boron-nitrogen interatomic distance and dihedral angle between the aromatic heterocycles. Calculated dipole moment of the adduct (7.17 D) is by 4.55 D over than the sum of dipole moments of the free components. Internal rotation barriers are not high: 1 kcal mol^?1 (0° and 180°) and 4 kcal mol^?1 (90°). The borabenzene-pyridine bonding energy (46 kcal mol^?1) is higher than that with dinitrogen (19 kcal mol^?1) and xenon atom (6 kcal mol^?1). The B-N bond length in the little stable adduct with dinitrogen is by 0.08 Å shorter than in the stable adduct with pyridine. The Lewis acid properties inherent in borabenzene are transferred on the π-electron system of pyridine fragment in the adduct. The electron transfer wavelength from borabenzene to pyridine fragment in argon matrix is by 109 nm higher than in tetrahydrofuran, as calculated by CIS CNDO/S method.     

Formation mechanism and conformational structure of 2,3,4-trimethyl-1,5-di(thiophen-2-yl)pentane-1,5-dione: quantum chemical study

The mechanism of formation of 1,5-diketone, a key intermediate in the stereoselective assembly of 2,3,4-trimethyl-7-methylidene-1,5-di(thiophen-2-yl)-6,8-dioxabicyclo[3.2.1]octane, and the conformational structures of the reagents and products were studied by quantum chemical calculations at the MP2/6-311++G**//B3LYP/6-31G* level of theory with solvent effects treated within the polarizable continuum model. The activation barrier for the addition of the 1-oxo-1-(thiophen-2-yl)propan-2-ide ion (1), which is generated from 1-(thiophen-2-yl)propan-1-one, to acetylene is 15.2 kcal mol^–1. The reaction affords β,γ-unsaturated ketone. The subsequent addition of carbanion 1 to the C=C double bond of the resulting β,γ-unsaturated ketons yields 1,5-diketone and occurs with insignificant (less than 1 kcal mol^–1) activation barrier.     

First Principles (DFT) Characterization of RhI/dppp‐Catalyzed CH Activation by Tandem 1,2‐Addition/1,4‐Rh Shift Reactions of Norbornene to Phenylboronic Acid

The C?H activation in the tandem, “merry‐go‐round”, [(dppp)Rh]‐catalyzed (dppp=1,3‐bis(diphenylphosphino)propane), four‐fold addition of norborene to PhB(OH)₂ has been postulated to occur by a C(alkyl)?H oxidative addition to square‐pyramidal Rh^III?H species, which in turn undergoes a C(aryl)?H reductive elimination. Our DFT calculations confirm the Rh^I/Rh^III mechanism. At the IEFPCM(toluene, 373.15 K)/PBE0/DGDZVP level of theory, the oxidative addition barrier was calculated to be 12.9 kcal mol^?1, and that of reductive elimination was 5.0 kcal mol^?1. The observed selectivity of the reaction correlates well with the relative energy barriers of the cycle steps. The higher barrier (20.9 kcal mol^?1) for norbornyl–Rh protonation ensures that the reaction is steered towards the 1,4‐shift (total barrier of 16.3 kcal mol^?1), acting as an equilibration shuttle. The carborhodation (13.2 kcal mol^?1) proceeds through a lower barrier than the protonation (16.7 kcal mol^?1) of the rearranged aryl–Rh species in the absence of o‐ or m‐substituents, ensuring multiple carborhodations take place. However, for 2,5‐dimethylphenyl, which was used as a model substrate, the barrier for carborhodation is increased to 19.4 kcal mol^?1, explaining the observed termination of the reaction at 1,2,3,4‐tetra(exo‐norborn‐2‐yl)benzene. Finally, calculations with (Z)‐2‐butene gave a carborhodation barrier of 20.2 kcal mol^?1, suggesting that carborhodation of non‐strained, open‐chain substrates would be disfavored relative to protonation.     

Quantum chemical modeling of superbase-catalyzed reactions of acetophenone and methyl mesityl ketone with acetylene

The mechanisms of furan formation and the competitive reaction of 1,5-diketone formation from 1-mesitylbut-2-en-1-one (1a) and 1-phenylbut-2-en-1-one (1b) were studied using the B3LYP/6-311++G**//B3LYP/6-31+G* quantum chemical approach taking into account solvation effects in terms of the IEFPCM model. The addition to 1a of the ethynide ion to form β-acetylene enolate ion (2a) occurs with the activation energy ΔG^≠ = 13.3 kcal mol^–1, while the further intramolecular O-vinylation with the closure of 2a to the dihydrofuran cycle of the dihydrofuran carbanion is the rate-determining step in the reaction pathway of substituted furan formation needing the activation energy G^≠ = 19.5 kcal mol^–1. The alternative addition of the mesitylethenolate ion to 1a to form the 1,5-diketone carbanion is associated with a higher (by 3.4 kcal mol^–1) free activation energy than that of ethynide ion addition. In contrast, in the case of 1b, the addition at the C=C bond of the phenylethenolate ion rather than of the ethynide ion to form the 1,5-diketone carbanion is more preferable, since its activation free energy is 1.5 kcal mol^–1 lower. The quantum chemical calculation results are consistent with the experimental data.     

Intramolecular nucleophilicS N 2 substitution at the tetrahedral carbon atom: Anab initio study

Pentacoordination of carbon atom in bicyclic organic compounds of the pentalene type was studied by theab initio RHF/6-31G^** and MP2(full)/6-31G^** methods. It was shown that intramolecularS _N 2 reactions with energy barriers within the energy scale of NMR spectroscopy can occur in systems in which a linear orientation of the attacking and leaving groups is realized. The barrier to the intramolecular nucleophilic substitution reaction in 2,3-dihydro-3-formylmethylenefuran is 36.9 (RHF) and 27.7 kcal mol⁻¹ (MP2) and decreases to 16.4 and 19.4 kcal mol⁻¹, respectively, in the case of diprotonation at the O atoms in this system. For model pentalene type compounds containing electron-deficient B atoms in the ring, theab initio calculations predict a further decrease in the barrier height (down to less than 10 kcal mol⁻¹). Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 7, pp. 1246–1256, July, 1999.     

Quantum-chemical study of the molecular forms of vanillin

Equilibrium structural parameters, dipole moments, relative energies, vibration spectra, and ionization potentials of various conformers of benzoid (B), p- and o-quinoid (Q), and deprotonated anionic forms of vanillin in a vacuum and in a polarizable medium with dielectric properties of water were calculated by the quantum-chemical method (U)B3LYP/cc-pVTZ. The intramolecular hydrogen bond in free vanillin benzoid molecule B1 is characterized by the energy of 4 kcal mol⁻¹ and by the barrier of cleavage 8 kcal mol⁻¹ that correspond to the conformational transition B1 → B2. The energy of the optimal p-quinoid conformer (Q1) is 22 kcal mol⁻¹ larger than the energy of B1 in a vacuum and 15 kcal mol⁻¹ in water. The p-quinoid forms greatly exceeds the benzoid forms by dipole moment, electrophilicity, and nucleophilicity. The structure calculated for the anion is intermediate between benzoid and p-quinoid forms, and the calculated energy of polarization stabilization in water is 57 kcal mol⁻¹.     

An ab initio molecular orbital study of the potential energy surface of the N2H → N2 + H system

The N₂H potential energy surface has been examined by ab initio molecular orbital theory using the 6-31G^** basis set with correlation energy evaluated by Møller—Plesset perturbation theory to fourth order. The ΔE for N₂H → N₂ + H is ?14.4 kcal mol^?1 and the barrier to dissociation is 10.5 kcal mol^?1. Inclusion of zero-point vibrational energies reduces the barrier to 5.8 kcal mol^?1.     

A Highly Oxidizing and Isolable Oxoruthenium(V) Complex [RuV(N4O)(O)]2+: Electronic Structure,Redox Properties,and Oxidation Reactions Investigated by DFT Calculations

The electronic structure and redox properties of the highly oxidizing, isolable Ru^V?O complex [Ru^V(N₄O)(O)]²⁺, its oxidation reactions with saturated alkanes (cyclohexane and methane) and inorganic substrates (hydrochloric acid and water), and its intermolecular coupling reaction have been examined by DFT calculations. The oxidation reactions with cyclohexane and methane proceed through hydrogen atom transfer in a transition state with a calculated free energy barrier of 10.8 and 23.8 kcal mol^?1, respectively. The overall free energy activation barrier (ΔG^≠=25.5 kcal mol^?1) of oxidation of hydrochloric acid can be decomposed into two parts: the formation of [Ru^III(N₄O)(HOCl)]²⁺ (ΔG=15.0 kcal mol^?1) and the substitution of HOCl by a water molecule (ΔG^≠=10.5 kcal mol^?1). For water oxidation, nucleophilic attack on Ru^V?O by water, leading to O? O bond formation, has a free energy barrier of 24.0 kcal mol^?1, the major component of which comes from the cleavage of the H? OH bond of water. Intermolecular self‐coupling of two molecules of [Ru^V(N₄O)(O)]²⁺ leads to the [(N₄O)Ru^IV? O₂? Ru^III(N₄O)]⁴⁺ complex with a calculated free energy barrier of 12.0 kcal mol^?1.     

Heterolysis of H2 Across a Classical Lewis Pair, 2,6‐Lutidine⋅BCl3: Synthesis,Characterization, and Mechanism

We report that 2,6‐lutidine?trichloroborane (Lut?BCl₃) reacts with H₂ in toluene, bromobenzene, dichloromethane, and Lut solvents producing the neutral hydride, Lut?BHCl₂. The mechanism was modeled with density functional theory, and energies of stationary states were calculated at the G3(MP2)B3 level of theory. Lut?BCl₃ was calculated to react with H₂ and form the ion pair, [LutH⁺][HBCl₃^?], with a barrier of ΔH^≠=24.7 kcal mol^?1 (ΔG^≠=29.8 kcal mol^?1). Metathesis with a second molecule of Lut?BCl₃ produced Lut?BHCl₂ and [LutH⁺][BCl₄^?]. The overall reaction is exothermic by 6.0 kcal mol^?1 (Δ_rG°=?1.1). Alternate pathways were explored involving the borenium cation (LutBCl₂⁺) and the four‐membered boracycle [(CH₂{NC₅H₃Me})BCl₂]. Barriers for addition of H₂ across the Lut/LutBCl₂⁺ pair and the boracycle B?C bond are substantially higher (ΔG^≠=42.1 and 49.4 kcal mol^?1, respectively), such that these pathways are excluded. The barrier for addition of H₂ to the boracycle B?N bond is comparable (ΔH^≠=28.5 and ΔG^≠=32 kcal mol^?1). Conversion of the intermediate 2‐(BHCl₂CH₂)‐6‐Me(C₅H₃NH) to Lut?BHCl₂ may occur by intermolecular steps involving proton/hydride transfers to Lut/BCl₃. Intramolecular protodeboronation, which could form Lut?BHCl₂ directly, is prohibited by a high barrier (ΔH^≠=52, ΔG^≠=51 kcal mol^?1).     

Different catalysis role of in‐loop and out‐of‐loop waters in assisting HNS/HSN proton transfer isomerizations: Bridging vs. surrounding effect

In this work, a density function theory (DFT) study is presented for the HNS/HSN isomerization assisted by 1–4 water molecules on the singlet state potential energy surface (PES). Two modes are considered to model the catalytic effect of these water molecules: (i) water molecule(s) participate directly in forming a proton transfer loop with HNS/HSN species, and (ii) water molecules are out of loop (referred to as out‐of‐loop waters) to assist the proton transfer. In the first mode, for the monohydration mechanism, the heat of reaction is 21.55 kcal · mol^?1 at the B3LYP/6‐311++G** level. The corresponding forward/backward barrier lowerings are obtained as 24.41/24.32 kcal · mol^?1 compared with the no‐water‐assisting isomerization barrier T (65.52/43.87 kcal · mol^?1). But when adding one water molecule on the HNS, there is another special proton‐transfer isomerization pathway with a transition state 10T′ in which the water is out of the proton transfer loop. The corresponding forward/backward barriers are 65.89/65.89 kcal · mol^?1. Clearly, this process is more difficult to follow than the R–T–P process. For the two‐water‐assisting mechanism, the heat of reaction is 19.61 kcal · mol^?1, and the forward/backward barriers are 32.27/12.66 kcal · mol^?1, decreased by 33.25/31.21 kcal · mol^?1 compared with T. For trihydration and tetrahydration, the forward/backward barriers decrease as 32.00/12.60 (30T) and 37.38/17.26 (40T) kcal · mol^?1, and the heat of reaction decreases by 19.39 and 19.23 kcal · mol^?1, compared with T, respectively. But, when four water molecules are involved in the reactant loop, the corresponding energy aspects increase compared with those of the trihydration. The forward/backward barriers are increased by 5.38 and 4.66 kcal · mol^?1 than the trihydration situation. In the second mode, the outer‐sphere water effect from the other water molecules directly H‐bonded to the loop is considered. When one to three water molecules attach to the looped water in one‐water in‐loop‐assisting proton transfer isomerization, their effects on the three energies are small, and the deviations are not more than 3 kcal · mol^?1 compared with the original monohydration‐assisting case. When adding one or two water molecules on the dihydration‐assisting mechanism, and increasing one water molecule on the trihydration, the corresponding energies also are not obviously changed. The results indicate that the forward/backward barriers for the three in‐loop water‐assisting case are the lowest, and the surrounding water molecules (out‐of‐loop) yield only a small effect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Oxidative Dehydrogenation of Propane over a VO2‐Exchanged MCM‐22 Zeolite: A DFT Study

The adsorption and the mechanism of the oxidative dehydrogenation (ODH) of propane over VO₂‐exchanged MCM‐22 are investigated by DFT calculations using the M06‐L functional, which takes into account dispersion contributions to the energy. The adsorption energies of propane are in good agreement with those from computationally much more demanding MP2 calculations and with experimental results. In contrast, B3LYP binding energies are too small. The reaction begins with the movement of a methylene hydrogen atom to the oxygen atom of the VO₂ group, which leads to an isopropyl radical bound to a HO? V? O intermediate. This step is rate determining with the apparent activation energy of 30.9 kcal mol^?1, a value within the range of experimental results for ODH over other silica supports. In the propene formation step, the hydroxyl group is the more reactive group requiring an apparent activation energy of 27.7 kcal mol^?1 compared to that of the oxy group of 40.8 kcal mol^?1. To take the effect of the extended framework into account, single‐point calculations on 120T structures at the same level of theory are performed. The apparent activation energy is reduced to 28.5 kcal mol^?1 by a stabilizing effect caused by the framework. Reoxidation of the catalyst is found to be important for the product release at the end of the reaction.     

On the Stability of Interactions between Pairs of Anions – Complexes of MCl3− (M=Be,Mg, Ca,Sr, Ba) with Pyridine and CN−

The ability of the central M atom of the MCl₃⁻ anion, with M=Be, Mg, Ca, Sr, Ba, to engage in a noncovalent bond with an approaching nucleophile is gauged by ab initio methods. The N atom of pyridine forms a M⋅⋅⋅N bond with an interaction energy between 12 and 21 kcal mol⁻¹, even though the π-hole above the M atom is not necessarily positive in sign. Despite a strong Coulombic repulsion between two anions, CN⁻ is also able to approach the M atom so as to engage in a metastable complex that is higher in energy than the individual anions. The energy barrier separating this complex from its constituent anion pair is roughly 20 kcal mol⁻¹. Despite the endothermic formation reaction energy of the CN⁻⋅⋅⋅MCl₃⁻ complex, the electron topology signals a strong interaction, more so than in pyridine⋅⋅⋅MCl₃⁻ with its exothermic binding energy. The dianionic complex is held together largely on the strength of interorbital interactions, thereby overcoming a repulsive electrostatic component. The latter is partially alleviated by the pyramidalization of the MCl₃ unit which makes its π-hole more positive. The complex sinks below the separate monomers in energy when the system is immersed in an aqueous medium, with a binding energy that varies from as much as 20 kcal mol⁻¹ for Be down to 1.2 kcal mol⁻¹ for Ba.     

Covalently Cross-Linked Watson–Crick Base Pair Models

Structural characteristics of Watson–Crick hydrogen-bonded base pairs are displayed by methylene-bridged base pairs of type A . The shown superposition of the X-ray structure obtained for the base pair A (Rib¹=Et; Rib²=Me) over that of a C–G base pair illustrates that A occupies an area similar to that occupied by a traditional Watson–Crick hydrogen-bonded base pair. Temperature-dependent ¹H NMR studies indicate that the energy barrier for rotation along its CH₂ bridge is about 10 kcal mol⁻¹, and that it exists predominantly in one conformer at −70°C.