Rate coefficients of the CF3CHFCF3 + H → CF3CFCF3 + H2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths

The minimum energy path (MEP) of the reaction, CF₃CHFCF₃ + H → transition state (TS) → CF₃CFCF₃ + H₂, has been computed at different ab initio levels and with density functional theory (DFT) using different functionals. The computed B3LYP/6‐31++G**, BH&HLYP/cc‐pVDZ, BMK/6‐31++G**, M05/6‐31+G**, M05‐2X/6‐31+G**, UMP2/6‐31++G**, PUMP2/6‐31++G**//UMP2/6‐31++G**, RCCSD(T)/aug‐cc‐pVDZ//UMP2/6‐31++G**, RCCSD(T)/aug‐cc‐pVTZ(spd,sp)//UMP2//6‐31++G**, RCCSD(T)/CBS//M05/6‐31+G**, and RCCSD(T)/CBS//UMP2/6‐31++G** MEPs, and associated gradients and Hessians, were used in reaction rate coefficient calculations based on the transition state theory (TST). Reaction rate coefficients were computed between 300 and 1500 K at various levels of TST, which include conventional TST, canonical variational TST (CVT) and improved CVT (ICVT), and with different tunneling corrections, namely, Wigner, zero‐curvature, and small‐curvature (SCT). The computed rate coefficients obtained at different ab initio, DFT and TST levels are compared with experimental values available in the 1000–1200 K temperature range. Based on the rate coefficients computed at the ICVT/SCT level, the highest TST level used in this study, the BH&HLYP functional performs best among all the functionals used, while the RCCSD(T)/CBS//MP2/6‐31++G** level is the best among all the ab initio levels used. Comparing computed reaction rate coefficients obtained at different levels of theory shows that, the computed barrier height has the strongest effect on the computed reaction rate coefficients as expected. Variational effects on the computed rate coefficients are found to be negligibly small. Although tunneling effects are relatively small at high temperatures (～1500 K), SCT corrections are significant at low temperatures (～300 K), and both barrier heights and the magnitudes of the imaginary frequencies affect SCT corrections. © 2012 Wiley Periodicals, Inc.     

PCM study of the solvent and substituent effects on bond dissociation energies of the C?NO bond

Quantum chemical calculations are used to estimate the equilibrium C? NO bond dissociation energies (BDEs) for eight X? NO molecule (X = CCl₃, C₆F₅, CH₃, CH₃CH₂, iC₃H₇, tC₄H₉, CH₂CHCH₂, and C₆H₅CH₂). These compounds are studied by employing the hybrid density functional theory (B3LYP, B3PW91, B3P86) methods together with 6‐31G** and 6‐311G** basis sets and the complete basis set (CBS‐QB3) method. The obtained results are compared with the available experimental results. It is demonstrated that B3P86/6‐31G** and CBS‐QB3 methods are accurate for computing the reliable BDEs for the X? NO molecule. Considering the inevitably computational cost of CBS‐QB3 method and the reliability of the B3P86 calculations, B3P86 method with 6‐31G** basis set may be more suitable to calculate the BDEs of the C? NO bond. The solvent effects on the BDEs of the C? NO bond are analyzed and it is shown that the C? NO BDEs in a vacuum computed by using B3PW91/6‐311G** method are the closest to the computed values in acetontrile and the average solvent effect is 1.48 kcal/mol. Subsequently, the substituent effects of the BDEs of the C? NO bond are further analyzed and it is found that electron denoting group stabilizes the radical and as a result BDE decreases; whereas electron withdrawing group stabilizes the group state of the molecule and thus increases the BDE from the parent molecule. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

A DFT study of hydride transfers to the carbonyl oxygen of DDQ

Hydride‐transfer reactions between benzylic substrates and 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ) were investigated by DFT (density functional theory) calculations. The lowest unoccupied molecular orbital of DDQ has the largest extension on two carbonyl oxygens, which comes from two‐step mixing of antisymmetric orbitals of fragment π MOs. Transition‐state (TS) geometries and activation energies of reactions of four benzylic substrates R²? CH₂‐para‐C₆H₄? R¹ (R¹, R² = H and/or OCH₃) with DDQ were calculated. M06‐2X/6‐311(+*)G* was found to be a practical computational method, giving energies and geometries similar to those of M06‐2X/6‐311++G(3df,2pd) and wB97xD/6‐311++G(3df,2pd). For toluene (R¹ = R² = H), an initiation‐propagation model was suggested, and the calculated kinetic isotope effect k(H)/k(D) = 5.0 with the tunnel correction at the propagating step is in good agreement with the experimental value 5.2. A reaction of para‐MeO? C₆H₄? CH₂(OMe) + DDQ + (H₂O)₁₄ → para‐MeO? C₆H₄? C(?O)H + HOMe + DDQH₂ + (H₂O)₁₃ was investigated by M06‐2X/6‐311(+*)G*. Four elementary processes were found and the hydride transfer (TS1) is the rate‐determining step. The hydride transfer was promoted by association with the water cluster. The size of the water cluster, (H₂O)_n, at TS1 was examined. Three models of n = 14, 20, and 26 were found to give similar activation energies. Metal‐free neutral hydride transfers from activated benzylic substrates to DDQ were proposed to be ready processes both kinetically and thermodynamically. © 2015 Wiley Periodicals, Inc.     

Density functional theory study of nitrogen‐14 nuclear quadrupole coupling parameters of L‐histidine: hydrogen‐bonded system

The calculations of nitrogen‐14 nuclear quadrupole parameters, nuclear quadrupole coupling constant, χ, and asymmetry parameter, η, of L‐His were done in two distinct environments: one as a free fully optimized molecule, an isolated molecule with the geometrical parameters taken from X‐ray, and the other in the orthorhombic and monoclinic solid states. The most probable interacting molecules with the central molecule in the crystalline phase were considered in the hexameric clusters to include hydrogen‐bonding effects in the calculations. The computations were performed with PW91P86/6‐31++G** and B3LYP6‐31++G** methods using the Gaussian 98 program. The good agreement between the nitrogen‐14 quadrupole parameters of the free His and imidazole molecules with their microwave available data demonstrates that the applied level of theory and the 6‐31++G** basis set are suitable to obtain reliable electric field gradient values. In the solid state, the shifts of quadrupole coupling parameters from the monomer to the solid phase are reasonably well reproduced for the amino and imino sites of imidazole ring in a hexameric cluster. That implies the fact that the hexameric cluster worked effectively to generate the results which are compatible with the experiment. The quadrupole coupling constant values of –N⁺H₃ group are in fair agreement with the experiment. This discrepancy is due to the absences of vibrational effects and the rotation of –N⁺H₃ group around N–C(α) bond. Copyright © 2012 John Wiley & Sons, Ltd.     

Computational Study of the Substitution Effect on the Mechanism for the Gold(I)‐Catalyzed Ring Expansions of Unactivated Alkynylcyclopropanes

The ring expansion reactions of unactivated alkynylcyclopropanes X‐C≡C‐C₃H₅ → X‐C=C₄H₅ (X = H, F, Cl, Me, OMe, NMe₂, CMe₃) were examined using the density functional theory calculations. All of the structures were completely optimized at the B3LYP/6‐311++G** level of theory. For clarify the effect of the cationic gold(I), we also added AuPH₃⁺ as the catalyst into the system and the structures for Au were calculated at the B3LYP/LANL2DZ level of theory. The main finding of this work is that the singlet‐triplet splitting of X‐C≡C‐C₃H₅ play an important role in determining the kinetic and thermodynamic stability of the unactivated ring expansion reactions. When X‐C≡C‐C₃H₅ with a smaller singlet‐triplet splitting is utilized, the reaction has a smaller activation energy and a larger exothermicity.     

Density functional evaluation and a feasibility study of intramolecular thione–thiol tautomerization

Performance of various density functionals for use in geometry and energetics calculation of thiocarbonyl systems is evaluated. The three biologically significant systems such as 2‐methyl‐3‐thiosemicarbazide, 1‐acetyl‐2‐thiohydantoin and bornane‐2‐thione are selected for the geometry analysis. Energy of tautomerization of thioacetone and enthalpy of formation of 2‐thiohydantoin are considered for analyzing the performance in energetics. Minnesota functionals such as M05‐2X, M06‐2X and range separated hybrid functional wB97 give best results in both geometry and energetics calculations. Studies on basis set effect showed reliable performance by 6‐31 + G* and 6‐31++G** over higher basis sets. Feasibility of tautomerization in the aforementioned thiones has been investigated using the best performing density functionals. The proposed thione–thiol tautomerization step during PPC‐DC catalyzed decarboxylation reaction has also been investigated and the computed high energy barrier shows less feasibility of the reaction.     

Theoretical prediction of the host–guest interactions between novel photoresponsive nanorings and C60: A strategy for facile encapsulation and release of fullerene

A series of photoresponsive‐group‐containing nanorings hosts with 12～14 Å in diameter is designed by introducing different number of azo groups as the structural composition units. And the host–guest interactions between fullerene C₆₀ and those nanoring hosts were investigated theoretically at M06‐2X/6‐31G(d)//M06‐L/MIDI! and wB97X‐D/6‐31G(d) levels. Analysis on geometrical characteristics and host–guest binding energies revealed that the designed nanoring molecule (labeled as 7 ) which is composed by seven azo groups and seven phenyls is the most feasible host for encapsulation of C₆₀ guest among all candidates. Moreover, inferring from the simulated UV‐vis‐NIR spectroscopy, the C₆₀ guest could be facilely released from the cavity of the host 7 via configuration transformation between trans‐form and cis‐form of the host under the 563 nm photoirradiation. Additionally, the frontier orbital features, weak interaction regions, infrared, and NMR spectra of the C₆₀@7 host–guest complex have also been investigated theoretically. © 2015 Wiley Periodicals, Inc.     

Quantum-Chemical Study of Alkyl Carbenium Ions in 100% Sulfuric Acid

A quantum-chemical study of neutral and protonated monoalkyl sulfates RHSO₄and [RH₂SO₄]⁺(where R = CH₃, C₂H₅, iso-C₃H₇, and tert-C₄H₉) is carried out. Calculations are performed using the Hartree–Fock method in the 6-31G** and 6-31++G** basis sets taking into account electron correlation according to the Müller–Plesset perturbation theory MP2/6-31+G*//6-31+G*. Protonated tert-butyl sulfate was also calculated by the DFT B3LYP/6-31++G** method. It was found that monoalkyl sulfates are covalent compounds, and the complete abstraction of alkyl carbenium ions from them has substantial energy cost: 196.4, 161.7, 150.8 and 136.0 kcal/mol, respectively. Protonated methyl and ethyl sulfates are also covalent compounds according to the calculation. They have lower but still high energies of heterolytic dissociation (65.0 and 33.5 kcal/mol, respectively). The energy of R⁺abstraction from protonated isopropyl sulfate is much lower: 23.6 kcal/mol. The main covalent state and the ion–molecular pair, which is a carbenium ion [C(CH₃)₂H]⁺solvated by the H₂SO₄molecule, have about the same energy. The ground state of protonated tert-butyl sulfate corresponds to the ion–molecular complex [C(CH₃)⁺ ₃H₂SO₄] with still lower energy of carbenium ion [C(CH₃)₃]⁺abstraction, which is equal to 10.0 kcal/mol. Calculation according to the DFT B3LYP/6-31++G** method shows the absence of a minimum for the protonated tert-butyl sulfate with a covalent structure on the potential energy surface.     

Computational study of tautomerism and aromaticity in mono‐ and dithio‐substituted tropolone

Keto‐enol tautomerism in mono‐ and dithio‐substituted analogs of tropolone was investigated using electronic structure computations. Seven structural isomers of C₇H₆OS and four of C₇H₆S₂ were optimized fully in gas phase at HF and B3LYP theoretical levels in combination with the 6‐311++g** basis set, as well as with the CBS‐QB3 and G3 methods. To examine the effects of an aqueous solvent on tautomeric equilibrium constants, each species was optimized in water using the self‐consistent reaction field polarizable continuum model at HF/6‐311++g** and B3LYP/6‐311++g** model chemistries. In both phases it was found that the enol forms were significantly more stable with respect to electronic energy and Gibbs free energy compared to the keto isomers, and outnumbered the keto species by several orders of magnitude. This was understood on the basis of elementary Hückel theory and the 4n + 2 rule, and supported by nucleus independent chemical shifts computations of NMR chemical shifts in these seven membered cyclic systems. © 2012 Wiley Periodicals, Inc.     

Halogen switching of azacarbenes C2NH ground states at ab initio and DFT levels

Relative stabilities and singlet–triplet energy differences are calculated for 24 C₂NX azacarbenes (where X is H, F, Cl, and Br). Three skeletal arrangements are employed including azacyclopropenylidene, [(imino)methylene]carbene, and cyanocarbene. Halogens appear to alternate the electronic ground states of C₂NH azacarbenes, from triplet to singlet states, at MP3/6‐311++G**, B1LYP/6‐311++G**, B3LYP/6‐311++G**, MP2/6‐311++G**, MP4(SDTQ)/6‐311++G**, QCISD(T)/6‐311++G**, CCSD(T)/6‐311++G**, CCSD(T)/cc‐pVTZ, G1, and G2 levels of theory. The aromatic characters of singlet cyclic azacyclopropenylidenes are measured using GIAO–NICS calculations. Linear correlations are found between the B3LYP/6‐311++G** calculated LUMO–HOMO energy gaps (ΔE_{HOMO ‐ LUMO}) of the singlet carbenes versus their corresponding singlet–triplet energy separations (ΔE). Electrophilic characters are found for all singlet azacarbenes in their addition reactions to alkenes with the highest electrophilicity being exhibited for X = F. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:377–388, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20442     

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (where n = 1, 2, 3), and protonated melamine with H₂O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6‐31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6‐31G(d), 6‐31 + G(d), 6‐31G(2df,p), and 6‐311++G(3df,3pd). B3LYP, M06, and ω B97XD calculations with 6‐31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6‐31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS‐QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3‐proton shift. The lowest overall activation energy, 111 kJ mol^?1 at G4MP2, was obtained for the deamination of melamine with 3H₂O/OH^?.     

DNA base stacking: The stacked uracil/uracil and thymine/thymine minima

The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)‐corrected M06‐2X/6‐31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4‐dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center‐of‐mass, whereas the other monomer remained still. Both face‐to‐back (one molecule exactly on top of the other) and face‐to‐face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas‐phase M06‐2X/6‐31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies. © 2012 Wiley Periodicals, Inc.     

The 1:1 glycine zwitterion-water complex: An ab initio electronic structure study

More than a dozen stationary points on the potential energy surface for the 1:1 glycine zwitterion—water complex have been investigated at Hartree-Fock or MP2 levels of theory with basis sets ranging from split valence (4-31G) to split valence plus polarization and diffuse function (6–31 + + G**) quality. Only one true minimum (GLYZWM, C₁ symmetry) could be located on the potential energy surface. GLYZWM features a bridged water molecule acting as both a hydrogen bond acceptor and donor with the NH₃⁻ and CO₂⁻ units of the glycine zwitterion. The total hydrogen bond energy in GLYZWM is computed as 16 kcal/mol (MP2/6–31 ++ G** // 6–31 ++ G**, including corrections for basis set superpositions errors). The computed vibrational frequencies and normal mode forms of the GLYZWM complex resemble in many cases experimental assignments made for the glycine zwitterion in bulk water on the basis of Raman spectroscopy. © 1996 by John Wiley & Sons, Inc.     

Buckycatcher polymer versus fullerene‐buckycatcher complex: Which is stronger?

The C₆₀H₂₈ buckycatcher (BC) is an excellent host for fullerenes. This receptor features two corannulene pincers which trap C₆₀/C₇₀ via π stacking interactions. Although, the formation of C₆₀@C₆₀H₂₈ complexes is readily observed, the dimerization of C₆₀H₂₈ is not a competitive process, even at high concentrations. By means of first principle calculations, we have studied the thermodynamics of the polymerization of BCs and the formation of fullerene complexes. The results obtained with the M06‐2X, B97‐D, B3LYP‐D3BJ, PBE‐D2, and PBE‐D3 functionals indicated that the interaction energy of (C₆₀H₂₈)₂ is larger than the one computed for C₆₀@C₆₀H₂₈, by 8–10 kcal/mol. Because of the greater number of atoms, and due to the presence of more hydrogens, the inclusion of free energy corrections lowers the energetic separation between (C₆₀H₂₈)₂ and C₆₀@C₆₀H₂₈, even though the dimer maintains its position as being slightly more bound than that of the C₆₀@C₆₀H₂₈. Our calculations indicated that up to the C₆₀H₂₈ trimer could be formed with a free energy change larger than that corresponding to the dimerization and fullerene complexation processes. Finally, we found that the inversion of the corannulene pincers attached to the cyclooctatetraene core is 2–3 kcal/mol lower than that corresponding to free corannulene. We expect that this work can motivate new investigations that may lead to the observation of C₆₀H₂₈ polymers. © 2015 Wiley Periodicals, Inc.     

Molecular structure and vibrational spectra of phenobaraitone by density functional theory and ab initio hartree-Fock calculations

Quantum chemistry calculations have been performed using Gaussian03 program to compute optimized geometry, harmonic vibrational frequency along with intensities in IR and Raman spectra at RHF/6-31++G** and B3LYP/6-31++G** levels for phenobarbitone (C₁₂H₁₂N₂O₃) in the ground state. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR and FT-Raman spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs) using MOLVIB program. A detailed interpretation of the infrared spectra of the title compound is reported. On the basis of the agreement between the calculated and observed results, the assignments of fundamental vibrational modes of phenobarbitone were examined and some assignments were proposed. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title compound have been constructed.     

Adsorption of polycyclic aromatic hydrocarbons and inversion barriers of curved conjugated systems inside the molecular cage ExCage6+

We investigated the hosting of planar and curved π systems by ExCage⁶⁺. The M06‐2X/6‐311G* method and including basis set superposition error (BSSE) corrections showed good agreement with the experimental free energy changes in solution. The mean absolute deviation (MAD) with respect to experiment was 1.3 kcal/mol. The M06‐2X/6‐31G* method exhibited a MAD of 2.1 kcal/mol, so it may be useful to investigate large systems. The good agreement between the M06‐2X/6‐311G*+BSSE results and the M06‐2X/6‐31G* ones was due to a fortuitous error cancelation between basis set incompleteness and BSSE. The interaction energies decreased linearly with the number of CC double bonds present in the PAH, but the shape of the PAH is an important factor in determining the binding strength. Finally, we studied how effective is ExCage⁶⁺ in reducing the inversion barriers of buckybowls. For corannulene, sumanene and dibenzo[a,g]corannulene they are reduced by 2.0, 2.7, and 2.0 kcal/mol, respectively. Although these values indicate an induced fit catalysis by ExCage⁶⁺, they are far from those values calculated inside bilayer graphene. Therefore, much work is necessary to replicate the reduction of inversion barriers observed for graphene.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

Density functional B3LYP and B3PW91 studies of the properties of four cyclic organodiboranes with tetramethylene fragments

Molecular structure and vibrational spectra of 1,2-tetramethylenediborane (B₂C₄H₁₂), 1,2:1,2-bis(tetramethylene)diborane (B₂C₈H₁₈), 1,1-tetramethylenediborane (B₂C₄H₁₂) and 1,1:2,2-bis(tetramethylene)diborane (B₂C₈H₁₈), have been studied using quantum computational density functional B3LYP and B3PW91 methods and 6-31G*, 6-31G** and 6-31++G** basis sets. Natural bond orbital analyses have been carried out to study in detail the nature of the B—C, C—C and B—H bonds in these molecules. This study showed that all these compounds are thermodynamically stable in the gas phase, but bicyclic structures are more stable than monocyclic structures.     

Anharmonic Effect of the Unimolecular Dissociation of Ethyl Radical

The anharmonic and harmonic rate constants have been calculated for the unimolecular dissociation of ethyl radical using the method proposed by Yao and Lin (YL method) at both B3LYP/6‐311++G** and MP2/6‐311++G** levels. The different rate constants indicate that the results obtained from B3LYP and MP2 method are very close. The anharmonic and tunneling effect of the title reaction has also been examined. The comparison shows that, both in microcanonical and canonical systems, the anharmonic rate constants are higher than those for harmonic cases, especially in the case of high total energies and temperatures, which indicates that anharmonic effect of the unimolecular dissociation of ethyl into C₂H₄ and H is so significant that cannot be neglected. The tunneling effect is very small for the decomposition of C₂H₅ radical.     

The Structure of 2-Methylphenylcyanamide in the Solid State

The structure of 2-methylphenylcyanamide NCNH(C₆H₄Me-2) is established in the solid state using single crystal X-ray diffraction data. The contribution of various intermolecular contacts to the crystal packing is studied using the Hirshfeld surface analysis and quantum chemical calculations within the density functional (DFT) M06-2X/6-311++G(d,p) level of theory.