Enthalpy of formation and bond energies on unsaturated oxygenated hydrocarbons using G3MP2B3 calculation methods

Enthalpies of unsaturated oxygenated hydrocarbons and radicals corresponding to the loss of hydrogen atoms from the parent molecules are intermediates and decomposition products in the oxidation and combustion of aromatic and polyaromatic species. Enthalpies (Δ_fH⁰₂₉₈) are calculated for a set of 27 oxygenated and nonoxygenated, unsaturated hydrocarbons and 12 radicals at the G3MP2B3 level of theory and with the commonly used B3LYP/6‐311g(d,p) density functional theory (DFT) method. Standard enthalpies of formation (Δ_fH⁰₂₉₈) are determined from the calculated enthalpy of reaction (ΔH⁰_rxn,298) using isodesmic work reactions with reference species that have accurately known Δ_fH⁰₂₉₈ values. The deviation between G3MP2B3 and B3LYP methods is under ±0.5 kcal mol^?1 for 9 species, 18 other species differs by less than ±1 kcal mol^?1 , and 11 species differ by about 1.5 kcal mol^?1. Under them are 11 radicals derived from the above‐oxygenated hydrocarbons that show good agreement between G3MP2B3 and B3LYP methods. G3 calculations have been performed to further validate enthalpy values, where a discrepancy of more than 2.5 kcal mol^?1 exists between the G3MP3B3 and density functional results. Surprisingly the G3 calculations support the density functional calculations in these several nonagreement cases. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 633–648, 2005     

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.     

Ligand Exchange Processes on Solvated Zinc Cations – DFT Analysis of Hydrogen Cyanide Exchange on [Zn(HCN)6]2+

The mechanisms for hydrogen cyanide exchange on [Zn(HCN)₆]²⁺ were studied using density functional theory (B3LYP/6‐311+G**), and showed that the limiting dissociative (D) pathway is more favorable than the associative interchange (I_a) mechanism. The activation barrier for the dissociative mechanism (7 kcal · mol^–1) is clearly lower than for the interchange mechanism (15.9 kcal · mol^–1).     

Thermochemical properties for n‐propyl,iso‐propyl,and tert‐butyl nitroalkanes,alkyl nitrites,and their carbon‐centered radicals

Density functional theory (DFT) based calculations are performed on a series of alkyl nitrites and nitroalkanes representing large‐scale primary, secondary, and tertiary nitro compounds and their radicals resulting from the loss of their skeletal hydrogen atoms. Geometries, vibration frequencies, and thermochemical properties [S°(T) and C°_p(T) (10 K ? T ? 5000 K)] are calculated at the B3LYP/6‐31G(d,p) DFT level. Δ_fH°₂₉₈ values are from B3LYP/6‐31G(d,p), B3LYP/6‐31+G(2d,2p), and the composite CBS‐QB3 levels. Potential energy barriers for the internal rotations have been computed at the B3LYP/6‐31G(d,p) level of theory, and the lower barrier contributions are incorporated into entropy and heat capacity data. The standard enthalpies of formation at 298 K are evaluated using isodesmic reaction schemes with several work reactions for each species. Recommended values derived from the most stable conformers of respective nitro‐ and nitrite isomers include ?30.57 and ?28.44 kcal mol^?1 for n‐propane‐, ?33.89 and ?32.32 kcal mol^?1 for iso‐propane‐, ?42.78 and ?41.36 kcal mol^?1 for tert‐butane‐nitro compounds and nitrites, respectively. Entropy and heat capacity values are also reported for the lower homologues: nitromethane, nitroethane, and corresponding nitrites. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 181–199, 2010     

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     

Hydrogen Cyanide Exchange on [Al(HCN)6]3+ – A DFT Study

The hydrogen cyanide exchange mechanism of [Al(HCN)₆]³⁺ has been investigated by DFT calculations (B3LYP/6‐311+G**). The calculations provide theoretical evidence that the hydrogen cyanide exchange proceeds via a limiting dissociative (D) mechanism involving a stable five‐coordinate intermediate [Al(HCN)₅ · (HCN)₂]³⁺. The activation energy for the D‐mechanism is 23.4 kcal · mol^–1, which is 2.8 kcal · mol^–1 lower than for the seven‐coordinate transition state [Al(HCN)₇]^3+? for the alternative associative (A) pathway. The difference in stability between the two intermediates [Al(HCN)₅ · (HCN)₂]³⁺ (12.1 kcal · mol^–1) and [Al(HCN)₇]³⁺ (25.7 kcal · mol^–1) in comparison to [Al(HCN)₆ · (HCN)]³⁺ is much more pronounced and further supports a limiting dissociative mechanism.     

(Pentafluoruphenyl)xenonium(II) cyanide, isocyanide, and fluoride in dichloromethane: A PCM/DFT study

Calculations by the PCM/B3LYP/6-311G++(3d₅f₇)&;Xe-3-111G(3d₅)PCM/B3LYP/6-311G-(3d₅f₇)&;Xe-3-111G(d₅) method show that, despite the higher electronegativity of the nitrogen atom, the interaction between the CN^? anion and the (pentaphenyl)xenonium(II) cation forms a xenon-carbon bond which is stronger by 6 kcal mol^?1 than the direct ionic bond between CN^? and Xe⁺.     

HCN exchange on [Cu(HCN)4]+: a quantum chemical investigation

Density functional (B3LYP, B3PW91, X3LYP, BP86, PBEPBE, PW91PW91, and M06) and ab initio (MP2, MP4sdq, CCSD, and CCSD(T)) calculations with extended basis sets (6-311+G**, TZVP, LANL2DZ+p, and SDD+p, the latter including extra polarization and diffuse functions) indicate that HCN exchange on [Cu(HCN)₄]⁺ proceeds via an associative interchange (I_a) mechanism and a D_3h transition structure {[Cu(HCN)₅]⁺}^?. The activation barrier, relative to the model complex [Cu(HCN)₄]⁺·HCN, varies modestly, depending on the computational level. Typical values are 8.0?kcal?M^?1 (B3LYP/6-311+G**), 6.0?kcal?M^?1 (M06/6-311+G**), and 4.8?kcal?M^?1 (CCSD(T)/6-311+G**//MP2(full)/6-311+G**). Inclusion of an implicit solvent model (B3LYP(CPCM)/6-311+G**) leads to an activation barrier of 5.8?kcal?mol^?1. Comparison of the HCN exchange mechanisms on [Li(HCN)₄]⁺ (limiting associative, A) and [Cu(HCN)₄]⁺ (associative interchange, I_a) reveals that π back donation in the equatorial Cu–N bonds in the transition state determines the mechanism.     

Ligand‐Exchange Processes on Solvated Beryllium Cations. Part III

On the basis of DFT calculations (B3LYP/6‐311+G**), the possibility to include solvent effects is considered in the investigation of the H₂O‐exchange mechanism on [Be(H₂O)₄]²⁺ within the widely used cluster approach. The smallest system in the gas phase, [Be(H₂O)₄(H₂O)]²⁺, shows the highest activation barrier of +15.6 kcal/mol, whereas the explicit addition of five H‐bonded H₂O molecules in [{Be(H₂O)₄(H₂O)}(H₂O)₅]²⁺ reduces the barrier to +13.5 kcal/mol. Single‐point calculations applying CPCM (B3LYP(CPCM:H₂O)/6‐311+G**//B3LYP/6‐311+G**) on [Be(H₂O)₄(H₂O)]²⁺ lower the barrier to +9.6 kcal/mol. Optimization of the precursor and transition state of [Be(H₂O)₄(H₂O)]²⁺ within an implicit model (B3LYP(CPCM:H₂O)/6‐311+G** or B3LYP(PCM:H₂O)/6‐311+G**) reduces the activation energy further to +8.3 kcal/mol but does not lead to any local minimum for the precursor and is, therefore, unfavorable.     

Synthesis and Theoretical Investigation of a 1,8‐Bis(bis(diisopropylamino)cyclopropeniminyl)naphthalene Proton Sponge Derivative

We report herein the synthesis and characterization of a new proton sponge derivative, 1,8‐bis(bis(diisopropylamino)cyclopropeniminyl)naphthalene 4 (DACN), as well as its bis‐protonated counterpart 6 . A crystal structure of 6 is presented, along with variable temperature ¹H NMR data on the BF₄^? salt ( 6?BF₄ ). DFT calculations were performed to investigate the structure of the monoprotonated species 7 and to gain insight into the structural and electronic nature of all three species. The proton affinity (PA) of 4 , calculated at the B3LYP/6‐311G++(d,p)//B3LYP/6‐31G(d,p) level, taking into account thermal corrections from the B3LYP/6‐31G(d,p) method, was 282.3 kcal mol^?1, while its pK_a was estimated at 27.0. NICS calculations were performed to examine the changes in aromaticity within these systems upon each successive protonation. Lastly, homodesmotic reaction schemes were used in order to estimate the factors contributing to the strong PA predicted for 4 .     

Evaluation of DFT Methods and Implicit Solvation Models for Anion‐Binding Host‐Guest Systems

Although supramolecular chemistry is traditionally an experimental discipline, computations have emerged as important tools for the understanding of supramolecules. We have explored how well commonly used density functional theory quantum mechanics and polarizable continuum solvation models can calculate binding affinities of host‐guest systems. We report the calculation of binding affinities for eight host–guest complexes and compare our results to experimentally measured binding free energies that span the range from ?2.3 to ?6.1 kcal mol^?1. These systems consist of four hosts (biotin[6]uril, triphenoxymethane, cryptand, and bis‐thiourea) with different halide ions (F^?, Cl^?, Br^?) in various media including organic and aqueous. The mean average deviation (MAD) of calculated from measured ΔG_a is 2.5 kcal mol^?1 when using B3LYP‐D3 with either CPCM or PCM. This MAD value lowers even more by eliminating two outliers: 1.1 kcal mol^?1 for CPCM and 1.2 kcal mol^?1 for PCM. The best DFT and implicit solvation model combination that we have studied is B3LYP?D3 with either CPCM or PCM.     

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.     

Vapor-phase Beckmann rearrangement of oxime molecules over H-Faujasite zeolite.

The Beckmann rearrangement (BR) plays an important role in a variety of industries. The mechanism of this reaction rearrangement of oximes with different molecular sizes, specifically, the oximes of formaldehyde (H₂C?NOH), Z‐acetaldehyde (CH₃HC?NOH), E‐acetaldehyde (CH₃HC?NOH) and acetone (CH₃)₂C?NOH, catalyzed by the Faujasite zeolite is investigated by both the quantum cluster and embedded cluster approaches at the B3LYP level of theory using the 6‐31G (d,p) basis set. To enhance the energetic properties, single point calculations are undertaken at MP2/6‐311G(d,p). The rearrangement step, using the bare cluster model, is the rate determining step of the entire reaction of these oxime molecules of which the energy barrier is between 50–70 kcal mol^?1. The more accurate embedded cluster model, in which the effect of the zeolitic framework is included, yields as the rate determining step, the formaldehyde oxime reaction rearrangement with an energy barrier of 50.4 kcal mol^?1. With the inclusion of the methyl substitution at the carbon‐end of formaldehyde oxime, the rate determining step of the reaction becomes the 1,2 H‐shift step for Z‐acetaldehyde oxime (30.5 kcal mol^?1) and acetone oxime (31.2 kcal mol^?1), while, in the E‐acetaldehyde oxime, the rate determining step is either the 1,2 H‐shift (26.2 kcal mol^?1) or the rearrangement step (26.6 kcal mol^?1). These results signify the important role that the effect of the zeolite framework plays in lowering the activation energy by stabilizing all of the ionic species in the process. It should, however, be noted that the sizeable turnover of a reaction catalyzed by the Brønsted acid site might be delayed by the quantitatively high desorption energy of the product and readsorption of the reactant at the active center.     

Deamination of the Radical Cation of the Base Moiety of 2′‐Deoxycytidine: A Theoretical Study

Five pathways leading to the deamination of cytosine (to uracil) after formation of its deprotonated radical cation are investigated in the gas phase, at the UB3LYP/6‐311G(d,p) level of theory, and in bulk aqueous solvent. The most favorable pathway involves hydrogen‐atom transfer from a water molecule to the N3 nitrogen of the deprotonated radical cation, followed by addition of the resulting hydroxyl radical to the C4 carbon of the cytosine derivative. Following protonation of the amino group (N4), the C4? N4 bond is broken with elimination of the NH₃^?+ radical and formation of a protonated uracil. The rate‐determining step of this mechanism is hydrogen‐atom transfer from a water molecule to the cytosine derivative. The associated free energy barrier is 70.2 kJ mol^?1.     

Preparing Gold(I) for Interactions with Proton Donors: The Elusive [Au]⋅⋅⋅HO Hydrogen Bond

MP2 and DFT calculations with correlation consistent basis sets indicate that isolated linear anionic dialkylgold(I) complexes form moderately strong (ca. 10 kcal mol^?1) Au???H hydrogen bonds with single H₂O molecules as donors in the absence of sterically demanding substituents. Relativistic effects are critically important in the attraction. Such bonds are significantly weaker in neutral, strong σ‐donor N‐heterocyclic carbene (NHC) complexes (ca. 5 kcal mol^?1). The overall association (>11 kcal mol^?1), however, is strengthened by co‐operative, synergistic classical hydrogen bonding when the NHC ligands bear NH units. Further manipulation of the interaction by ligands positioned trans to the carbene, is possible.     

Ethyl 3‐[1‐(5,5‐dimethyl‐2‐oxo‐1,3,2‐dioxaphosphorin‐2‐yl)propan‐2‐ylidene]carbazate: a combined X‐ray and density functional theory (DFT) study

In the title compound, C₁₁H₂₁N₂O₅P, one of the two carbazate N atoms is involved in the C=N double bond and the H atom of the second N atom is engaged in an intramolecular hydrogen bond with an O atom from the dimethylphosphorin‐2‐yl group, which is in an uncommon cis position with respect to the carbamate group. The cohesion of the crystal structure is also reinforced by weak intermolecular hydrogen bonds. Density functional theory (DFT) calculations at the B3LYP/6‐311++g(2d,2p) level revealed the lowest energy structure to have a Z configuration at the C=N bond, which is consistent with the configuration found in the X‐ray crystal structure, as well as a less stable E counterpart which lies 2.0 kcal mol⁻¹ higher in potential energy. Correlations between the experimental and computational studies are discussed.     

Theoretical Investigation of the Interaction between Carbon Monoxide and Carbon Nanotubes with Single‐Vacancy Defects

Density functional theory calculations are used to study the healing process of a defective CNT (i.e. (8,0) CNT) by CO molecules. The healing undergoes three evolutionary steps: 1) the chemisorption of the first CO molecule, 2) the incorporation of the C atom of CO into the CNT, accompanied by the adsorption of the leaving O atom on the CNT surface, 3) the removal of the adsorbed O atom from the CNT surface by a second CO molecule to form CO₂ and the perfect CNT. Overall, adsorption of the first CO reveals a barrier of 2.99 kcal mol^?1 and is strongly exothermal by 109.11 kcal mol^?1, while adsorption of a second CO has an intrinsic barrier of 32.37 kcal mol^?1and is exothermal by 62.34 kcal mol^?1. In light of the unique conditions of CNT synthesis, that is, high temperatures in a closed container, the healing of the defective CNT could be effective in the presence of CO molecules. Therefore, we propose that among the available CNT synthesis procedures, the good performance of chemical vapor decomposition of CO on metal nanoparticles might be ascribed to the dual role of CO, that is, CO acts both as a carbon source and a defect healer. The present results are expected to help a deeper understanding of CNT growth.     

Investigation on the Mechanism for C–N Coupling of 3‐Iodopyridine and Pyrazole Catalyzed by Cu(I)

The reaction mechanism for C–N coupling of 3‐iodopyridine and pyrazole catalyzed by Cu(I) was studied by the density functional theory. All of the reactants, intermediates, transition states, and products were optimized with the B3LYP method at 6–31+G(d) basis set. The single‐point energy and zero‐point energy correction were calculated for the optimized configuration of each compound with the sane method at 6–311++G(d,p) basis set. Transition states have been confirmed by the corresponding vibration analysis and intrinsic reactions coordinate. In addition, nature bond orbital and atoms in molecules (AIM) theories have been used to analyze orbital interactions and bond natures. The results showed that the activation energy of the rate‐determining step in the absence of catalysts was 250.63 kJ·mol^?1, which were 74.01 and 131.68 kJ·mol^?1 via Cu₂O and CuI catalyzed, respectively. Results indicated that catalyst Cu₂O promotes reaction effectively. All calculations were consistent with experiments.     

A structural and theoretical study of the intermolecular interactions in 8‐hydroxyquinolinium‐7‐carboxylate monohydrate

In the title compound, C₁₀H₇NO₃·H₂O, the zwitterionic organic molecules and the water molecules are connected by N—H...O and O—H...O hydrogen bonds to form ribbons, and π–π stacking interactions expand these ribbons into a three‐dimensional net. The energies of these hydrogen bonds adopt values typical for mildly weak interactions (3.33–7.75 kcal mol⁻¹; 1 kcal mol⁻¹ = 4.184 kJ mol⁻¹). The total π–π stacking interactions between aromatic molecules can be classified as mildly strong (energies of 15.3 and 33.9 kcal mol⁻¹), and they are made up of multiple constituent π–π interactions between six‐membered rings. The short intermolecular C—H...O contact between two zwitterionic molecules is nonbonding in character.     

新的杯[4]芳烃衍生物通过缔合乙腈进行自插入的X-射线衍射和密度泛函理论研究

合成和表征了一个新的杯[4]芳烃衍生物，11,23-二羟亚胺甲基-25,27-二羟基-26,28-二丙氧基杯[4]芳烃 (B)及其与乙腈生成的组成为B·2CH₃CN的化合物。¹H NMR显示，在B·2CH₃CN中B采取锥型构象，X-射线衍射分析确证在溶液中所发现的构象。在晶格网络中存在着B·2CH₃CN以二聚体形式的自插入现象。在B3LYP/6-311G(d)水平上计算了该自插入二聚体中的非共价相互作用能，并对基集叠加误差进行了校正。在二聚体中的B·2CH₃CN，一个CH₃CN通过与羟亚胺基形成氢键使之稳定，结合能为–5.02 kJ·mol^-1，另一个CH₃CN则通过与另一个羟亚胺基形成氢键以及与另一B·2CH₃CN中B苯环空腔间的C–H···π相互作用使之稳定，结合能分别为–14.23 kJ·mol^-1和–3.77 kJ·mol^-1。自插入的驱动能为–7.54 kJ·mol^-1。