DFT study on the mechanism of trimolecular radical reactions: isomerisation in small clusters

ABSTRACT

Structural and thermodynamic properties of 48 trimolecular clusters containing one radicl and two protic molecules (H₂O, NH₃, H₂O₂, CH₃OH, HOCl) were studied at B3LYP/6-311++G(3df,3pd) level of theory. These radical-clusters have non-cyclic structures and are stabilised via two inter-molecular hydrogen bonding interactions. The calculated enthalpies of formation of the radical-clusters were generally in the range of ?30 to ?50 kJ/mol. The calculated activation energies (E_a) of the intra-cluster hydrogen transfers were smaller than 70 kJ/mol. Also, structures and thermodynamics of 15 cyclic molecular clusters as well as multi-hydrogen transfers in them were investigated. The results showed that the stability of the cyclic clusters and activation energies of the multi-hydrogen transfers depend on the cluster size.     

Natural bond orbital (NBO) analysis of the angular group induced bond alternation (AGIBA) substituent effect

The geometries, natural charges, and resonance structures of 11 monosubstituted benzene derivatives were analyzed at the B3LYP/6‐311++G(d,p) and HF/6‐311++G(d, p) levels of theory. The following angular substituents were chosen: OCH₃, CH₂CH₃, OH, SH, NHCH₃, NHNH₂, N?O, CH?CH₂, N?CH₂, N?NH, and CHO. The analysis of resonance structures was performed by using two different methodologies: harmonic oscillator stabilization energies (HOSE) and natural resonance theory (NRT). Also, the natural bond orbital (NBO) donor–acceptor stabilization energies for different resonance structures were calculated. We found that for all the substituents, the purely geometric resonance stabilization parameter (HOSE) is linearly correlated with quantum chemically derived resonance structure weight (NRT) of a given structure. Also, the calculations provide qualitative support for the earlier assumption of a through space angular group induced bond alternation (AGIBA) effect. Copyright © 2010 John Wiley & Sons, Ltd.     

Quantum chemical studies of the OH-initiated oxidation reactions of propenols in the presence of O2

ABSTRACT

The atmospheric oxidation mechanisms of 1- and 2-propenol initiated by OH radical have been theoretically investigated at the CCSD(T)//BH&;HLYP/6-311?+?+G(d,p) level of theory. Conventional transition state theory was employed to predict the rate constants for the initial reaction channels. The calculations clearly indicate that OH-addition channels contribute maximum to the total reaction, both for 1- and 2-propenol, while H-abstraction channels can be neglected at the temperature range of 220–520?K. The calculated total rate constants at 298?K are 1.66?×?10^?11 and 7.69?×?10^?12 cm³?molecule^?1?s^?1 respectively for 1- and 2-propenol, which are in reasonable agreement with the experimental values of similar systems (vinyl ethers?+?OH reactions). The deduced Arrhenius expressions are k(OH?+?1-propenol)?=?1.43?×?10^?12 exp[(743.7?K)/T] and k(OH?+?2-propenol)?=?2.86?×?10^?12 exp[(310.5?K)/T] cm³?molecule^?1?s^?1. Under atmospheric condition, the OH-addition intermediates (CH₃C?HCH(OH)₂, CH₃CH(OH)C?H(OH), CH₃CH(OH)₂?CH₂, CH₃?C(OH)CH₂(OH)) are likely to react rapidly with O₂, the theoretically identified major products for 1-propenol are HCOOH, CH₃CHO and CH₃CH(OH)CHO, and the dominant products for 2-propenol are CH₃COOH, HCHO and CH₃COCH₂OH, both companied with the regeneration of OH and HO₂ radicals (crucial reactive radicals in the atmosphere).     

Tuning of carbon bonds by substituent effects: an ab initio study

ABSTRACT

An ab initio study, at the MP2/aug-cc-pVTZ level of theory, is performed to study σ-hole bond in binary XH₃C···CNY complexes, where X = CN, F, NO₂, CCH and Y = H, OH, NH₂, CH₃, C₂H₅, Li. This type of interaction is labelled as ‘carbon bond’, since a covalently bonded carbon atom acts as the Lewis acid in these systems. The geometrical and energetic parameters of the resulting complexes are analysed in details. The interaction energies of these complexes are between ?4.97 kJ/mol in (HCC)H₃C···CNH and ?23.07 kJ/mol in (O₂N)H₃C···CNLi. It is found that the electrostatic interaction plays a key role in the overall stabilisation of these carbon-bonded complexes. To deepen the understanding of the nature of the carbon-bonding, the molecular electrostatic potential, natural bond orbital, quantum theory of atoms in molecules and non-covalent interaction index analyses are also used. Our results indicate that the carbon bond is favoured over the C-H···C hydrogen bond in the all complexes considered and may suggest the possible important roles of the C···C interactions in the crystal growth and design.     

A theoretical study of substitution effects on halogen–π interactions

Ab initio calculations are performed to analyse the existence of intermolecular halogen···π interactions in NCX complexes with YC≡CY, where X = Cl, Br and Y = H, CN, F, Cl, OH, NH₂, and CH₃. Molecular geometries and interaction energies of the complexes are investigated at the MP2/aug-cc-pVTZ level of theory. Our results indicate that the interaction energies for the NCX···YC≡CY complexes lie in the range between ?0.5 and ?5.9 kcal/mol. The physical nature of the interactions is studied using symmetry-adapted perturbation theory (SAPT). The stability of the X···π interactions is predicted to be attributable mainly to electrostatic and dispersion effects.     

Regium bonds formed by MX (M═Cu,Ag, Au; X═F,Cl, Br) with phosphine-oxide/phosphinous acid: comparisons between oxygen-shared and phosphine-shared complexes

ABSTRACT

Regium bonds interaction between phosphine oxide (H₃PO), the trans phosphinuous acid (T-PH₂OH), the cis phosphinuous acid (C-PH₂OH) and MX (M═Cu, Ag, Au; X═F, Cl, Br) complexes were investigated by means of ab initio MP2/aug-cc-pVTZ method. For phosphinuous acid and MX complexes, two types of regium bonded interaction (trans and cis complexes) are observed and the two types of structures are very easily transformed from one type to another due to a low energy barrier. The molecular interaction energies are in the order of Au?>?Cu?>?Ag, F?>?Cl?>?Br and increase with the decrease of intermolecular distance R_int. Two resonance-type structures of P:M-X (ωI) ? P–M:X (ωII), O:M-X (ωI) ? O–M:X (ωII) are recognised by the natural resonance theory (NRT) and the natural bond orbitals (NBOs) analysis. The competition between ωI ? ωII resonance structures mainly arises from hyperconjugation interactions, in all phosphor-shared complexes, P–M:X resonance accounts for a larger proportion which leads to the covalent characters. All of complexes have been described in terms of their electron density properties.     

C 78 IPR fullerenes: Computed B3LYP/6-31G*//HF/3-21G temperature-dependent relative concentrations

The five isolated-pentagon-rule (IPR) satisfying isomers of C₇₈, labeled 1-5, or according to symmetry as D₃, C_2v, C' _2v , D_3h, and D' _3h , are computed. The cage geometries are optimized at the ab initio HF level with the standard 3-21G basis set (HF/3-21G). The separation energetics is then computed using the B3LYP density-functional treatment in the standard 6-31G* basis set (B3LYP/6-31G*//HF/3-21G). Harmonic vibrational frequencies are calculated by the SAM1 semiempirical method. The computed energies, structural and vibrational data are employed in the construction of isomeric partition functions and evaluation of the relative Gibbs free energies. The results are converted into relative concentrations for a wide temperature interval. The C' _2v structure is the most populated throughout while the D_3h species is negligible at all temperatures. The agreement between theory and experiment is reasonable, though some aspects are still to be clarified. Received 28 November 2000     

The Application of Raman Spectroscopy to the Study of the Uranyl Mineral Coconinoite Fe2Al2(UO2)2(PO4)4(SO4)(OH)2 · 20H2O

ABSTRACT

Raman spectra of the uranyl-containing mineral coconinoite, Fe₂Al₂(UO₂)₂(PO₄)₄(SO₄)(OH)₂ · 20H₂O, are presented and compared with the mineral's infrared spectra. Bands connected with (UO₂)²⁺, (PO₄)^3?, (SO₄)^2?, (OH)^?, and H₂O stretching and bending vibrations are assigned. Approximate U?O bond lengths in uranyl, (UO₂)²⁺, and O?H…O hydrogen bond lengths are calculated from the wavenumbers of the U?O stretching vibrations and (OH)^? and H₂O stretching vibrations, respectively, and compared with published data for similar natural and synthetic compounds.     

Shell-model calculations on Ni and Cu isotopes

Binding energies, excitation energies and spectroscopic factors have been calculated for^57–67Ni and^58–68Cu in an unrestricted (2p_3/2, lf _5/2,2p_1/2) shell-model space. The effective two-body matrix elements are obtained from the modified surface delta interaction (MSDI) and from a least-squares fit to experimental binding and excitation energies (ASDI). The average deviation between about 100 experimental and calculated energies is 0.14MeV for MSDI and 0.08 MeV for ASDI. Excitation energies of high-spin states are given also. Spectroscopic factors have been calculated for all single-nucleon transfer reactions on stable Ni or Cu targets leading to Ni or Cu isotopes. For spectroscopic factors larger than 0.4 the average deviation between theory and experiment is about 30%. The experimentally observed and calculated spectroscopic strengths are compared by using sum rules and are found to be consistent. An extensive compilation has been made of experimental data on energies,J ^π assignments and spectroscopic factors.     

Prediction and characterisation of a chalcogen···π interaction with acetylene as a potential electron donor in XHS···HCCH and XHSe···HCCH (X = F,Cl, Br,CN, OH,OCH3, NH2, CH3) σ-hole complexes

It is well-known that many covalently bonded atoms of group VI have specific positive regions of electrostatic potential (σ-holes) through which they can interact with Lewis bases. This interaction is called ‘chalcogen bond’ by analogy with halogen bond and hydrogen bond. In this study, ab initio calculations are performed to predict and characterise chalcogen···π interactions in XHS···HCCH and XHSe···HCCH complexes, where X = F, Cl, Br, CN, OH, OCH₃, NH₂, CH₃. For the complexes studied here, XHS(Se) and HCCH are treated as a Lewis acid and a Lewis base, respectively. The CCSD(T)/aug-cc-pVTZ interaction energies of this type of σ-hole bonding range from ?1.18 to ?4.83 kcal/mol. The calculated interaction energies tend to increase in magnitude with increasing positive electrostatic potential on the extension of X–S(Se) bond. The stability of chalcogen···π complexes is attributed mainly to electrostatic and correlation effects. The nature of chalcogen···π interactions is unveiled by means of the atoms in molecules, natural bond orbital, and electron localisation function analyses.     

Structural and thermochemical properties of methyl ethyl sulfide alcohols: HOCH2SCH2CH3, CH3SCH(OH)CH3, CH3SCH2CH2OH,and radicals corresponding to loss of H atom

Sulfide alkoxy radicals are important intermediates during the partial oxidation of alkyl sulfides in atmospheric chemistry and in combustion. The atmospheric reaction sequence to formation of the alkoxy radicals includes (1) initial reaction with OH to create a radical on a carbon site, (2) the carbon radical then associates with ³O₂ to form a peroxy radical, and (3) an NO radical reacts with the peroxy radical to form an alkoxy radical (RO?) plus NO₂. This study determines structural parameters, internal rotor potentials, bond dissociation energies, and thermochemical properties (Δ_fH°, S°, and C_p(T)) of 3 corresponding alcohols HOCH₂SCH₂CH₃, CH₃SCH(OH)CH₃, and CH₃SCH₂CH₂OH of methyl ethyl sulfides studied in order to characterize the thermochemistry of the respective alkoxy radicals. The lowest energy molecular structures were calculated using the B3LYP density functional level of theory with the 6‐311G(2d,d,p) basis set. Standard enthalpies of formation (Δ_fH°₂₉₈) for the radicals and their parent molecules were calculated using B3LYP/6‐31 + G(2d,p), CBS‐QB3, M062x/6‐311 + g(2d,p), and G3MP2B3 methods. Isodesmic reactions were used to determine ?_fH° values. Internal rotation potential energy diagrams and rotation barriers were investigated using the B3LYP/6‐31 + G(d,p) level theory. The contributions for S°₂₉₈ and C_p(T) were calculated using the rigid rotor harmonic oscillator approximation based on the structures and vibrational frequencies obtained by CBS‐QB3 calculations, with contributions from torsion frequencies replaced by internal rotor contributions. Group additivity and hydrogen bond increment values were developed for estimating properties of structurally similar and larger sulfur‐containing peroxide molecules and their radicals.     

Quantum chemical studies of the solvation of the hydroxide ion

Abstract

To understand and model the solvation of the hydroxide ion, OH(H₂O)^? _n clusters, n = 1?5, are studied using ab initio quantum chemical techniques, largely at the MP2 level of theory using a double zeta plus polarization functions basis extended by diffuse functions. Energies and vibrational frequencies, together with thermodynamic quantities such as enthalpies, entropies and Gibbs free energies, are computed. This permits comparison with experimental estimates of the successive thermodynamic changes associated with the reaction OH(H₂O)^? _n + H₂O → OH(H₂O)^? _n+1. The theoretical values are in good agreement with experiment. The free energy of hydration of OH^? is modelled by a composite discrete-continuum method where the effects of the first hydration shell (n = 3) are obtained from the gas phase cluster calculation, while the long-range effects are modelled using self consistent reaction field theory, namely by calculating the solvation energy of OH(H₂O)^? _n in a dielectric continuum. The best estimate of the solvation (free) energy at 298 K is ?84·5 kcal mol^?1, compared to the experimental value of ?102·8 kcal mol^?1.     

Theoretical study on the mechanism and kinetics of atmospheric reactions NH2OH + OOH and NH2CH3 + OOH

Mechanism and kinetics of NH₂OH + OOH and NH₂CH₃ + OOH reactions were studied at the B3LYP and M062X levels of theory using the 6-311++G(3df, 3pd) basis set. The NH₂OH + OOH and NH₂CH₃ + OOH reactions proceed through different paths which lead to different products. Transition state structure and activation energy of each path were calculated. The calculated activation energies of hydrogen abstraction reactions were smaller than 25 kcal/mol and of substitution reactions are in the range of 50–70 kcal/mol. The rate constants were calculated using transition state theory (TST) modified for tunneling effect at 273–2000 K.     

Acid‐base properties and supramolecular structure of N‐[(hydroxymethyl)triazolyl]triflamides: DFT,ab initio,and FTIR study

For N‐{[2‐(hydroxymethyl)‐2H‐1,2,3‐triazolyl‐4‐yl]methyl}triflamide 1 , N‐{[2‐(hydroxymethyl)‐2H‐1,2,3‐triazolyl‐4‐yl]methyl}‐N‐phenyltriflamide 2 , and N,N‐bis{[2‐(hydroxymethyl)‐2H‐1,2,3‐triazolyl‐4‐yl]methyl}triflamide 3 , the proton affinities of the triazole nitrogen atoms and the hydroxy and sulfonyl oxygen atoms as well as the energies of formation of the conformers with intramolecular H‐bonds and dimers with intermolecular NH?N, OH?N, OH?O═S, and NH?O═S H‐bonds were calculated by density functional theory and second‐order Møller‐Plesset perturbation methods. Quantum Theory of Atoms in Molecules analysis was performed to investigate the nature of H‐bonds. According to Fourier transform infrared spectroscopy, in CH₂Cl₂ solution, the monomeric molecules of 1 to 3 exist in the equilibrium with cyclic dimers having the OH?N hydrogen bonds.     

Density functional investigation of metal encapsulated X@C12Si8 heterofullerene (X=Li, Na, K, Be, Mg, Ca, Al, Ga)

The stability and the possible application of our recently reported SiC heterofullerenes inspire the investigation of their further stabilization through ion encapsulation. The endohedral complexes X@C₁₂Si₈, where X=Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, Ca²⁺, Al³⁺, and Ga³⁺, are probed at the MPWB1K/6-311G? and B3LYP/6-311G* levels of theory. The optimized geometries show the expanding or contracting capability of C₁₂Si₈ in order to accommodate metal ion guests. The inclusion energies indicate the stability of the complexes compared to the components. Meanwhile, the calculated binding energies show the stabilization of C₁₂Si₈ through the inclusion of Be²⁺, Mg²⁺, Al³⁺, and Ga³⁺. The host-guest interaction that is probed through NBO atomic charges supports the obtained results. This study refers to “metal ion encapsulation” as a strategy for stabilization of SiC heterofullerenes.     

Symmetric bifurcated halogen bonds: substituent and cooperative effects

ABSTRACT

The aim of this study is to investigate the geometries, interaction energies and bonding properties of the symmetrical bifurcated halogen bond interactions (BXBs) by means of ab initio calculations. For this purpose, the NCX (X = Cl, Br) molecule is paired with a series of N-formyl formamide (NFF) derivatives (NFF-Z, Z = H, CN, CCH, OH, CH₃ and Li), and the properties of the resulting complexes are studied by molecular electrostatic potential, quantum theory of atoms in molecules, noncovalent interaction index and natural bond orbital analyses. For a fixed NCX molecule, interaction energies increase in the order of Z = Li > CH₃ > H > OH > CCH > CN. We found a strong correlation between the interaction energies of NCX:NFF-Z complexes and molecular electrostatic potential minimum values associated with NFF-Z monomers. Moreover, cooperative effects between BXB and X???N halogen bond interactions are studied in the ternary NCX:NCX:NFF-Z systems. Our results indicate that the strength of BXB interactions in the ternary complexes is enhanced by the presence of X???N bonds. Besides, cooperativity effects tend to increase the covalency of BXBs in these systems.     

Atomic and molecular adsorption on Pd(111)

The adsorption properties of a variety of atomic species (H, O, N, S, and C), molecular species (N₂, HCN, CO, NO, and NH₃) and molecular fragments (CN, NH₂, NH, CH₃, CH₂, CH, HNO, NOH, and OH) are calculated on the (111) facet of palladium using periodic self-consistent density functional theory (DFT–GGA) calculations at ¼ ML coverage. For each species, we determine the optimal binding geometry and corresponding binding energy. The vibrational frequencies of these adsorbed species are calculated and are found to be in good agreement with experimental values that have been reported in literature. From the binding energies, we calculate potential energy surfaces for the decomposition of NO, CO, N₂, NH₃, and CH₄ on Pd(111), showing that only the decomposition of NO is thermochemically preferred to its molecular desorption.     

Thermochemistry,bond energies and internal rotor barriers of methyl sulfinic acid,methyl sulfinic acid ester and their radicals

Sulfur–Oxygen containing hydrocarbons are formed in oxidation of sulfides and thiols in the atmosphere, on aerosols and in combustion processes. Understanding their thermochemical properties is important to evaluate their formation and transformation paths. Structures, thermochemical properties, bond energies, and internal rotor potentials of methyl sulfinic acid CH₃S(?O)OH, its methyl ester CH₃S(?O)OCH₃ and radicals corresponding to loss of a hydrogen atom have been studied. Gas phase standard enthalpies of formation and bond energies were calculated using B3LYP/6‐311G (2d, p) individual and CBS‐QB3 composite methods employing work reactions to further improve accuracy of the ${\Delta} _{{\bf f}} H_{{\bf 298}}^{{\bf o}} $ . Molecular structures, vibration frequencies, and internal rotor potentials were calculated. Enthalpies of the parent molecules CH₃S(?O)OH and CH₃S(?O)OCH₃ are evaluated as ?77.4 and ?72.7 kcal mol^?1 at the CBS? QB3 level; Enthalpies of radicals C^?H₂? S(?O)? OH, CH₃? S^?(?O)₂, C^?H₂? S(?O)? OCH₃ and CH₃? S(?O)? OC^?H₂ (CBS‐QB3) are ?25.7, ?52.3, ?22.8, and ?26.8 kcal mol^?1, respectively. The CH₃C(?O)O—H bond dissociation energy is of 77.1 kcal mol^?1. Two of the intermediate radicals are unstable and rapidly dissociate. The CH₃S(?O)? O. radical obtained from the parent CH₃? S(?O)? OH dissociates into methyl radical (${\bf CH}_{{\bf 3}}^{{\bf .}} $ ) plus SO₂ with endothermicity (ΔH_rxn) of only 16.2 kcal mol^?1. The CH₃? S(?O)? OC^?H₂ radical dissociates into CH₃? S^?=O and CH₂=O with little or no barrier and an exothermicity of ?19.9 kcal mol^?1. DFT and the Complete Basis Set‐QB3 enthalpy values are in close agreement; this accord is attributed to use of isodesmic work reactions for the analysis and suggests this combination of B3LYP/work reaction approach is acceptable for larger molecules. Copyright © 2010 John Wiley & Sons, Ltd.     

Adsorption sensitivity of pristine and Al- or Si-doped boron nitride nanoflake to COCl2: a DFT study

ABSTRACT

The adsorption of phosgene (COCl₂) on pristine, Al- and Si-doped boron nitride nanoflakes (BNNFs) is studied using density functional theory calculations. The adsorption energies of the most stable complexes, formed from interaction between COCl₂ and the pristine, Al- and Si-doped BNNFs are ?28.97, ?78.71 and ?171.60?kJ/mol at the M06-2X/6-31?+?G* level of theory, respectively. It is found that COCl₂ experiences a chemisorption interaction over the doped BNNFs, significantly altering its structure with respect to the gas-phase molecule. The COCl₂ adsorption can also induce a change in the HOMO–LUMO or SOMO–LUMO energy gap of the surface. In particular, the adsorption of COCl₂ is found to decrease the HOMO–LUMO energy gap of Al-doped BNNF by about 30%. It is suggested that the Al- or Si-doped BNNFs can be considered as a potential material for detecting toxic COCl₂.     

Long-range Rydberg-Rydberg interactions and molecular resonances

We present a detailed theoretical treatment to describe the lineshape of molecular resonances in a cold dense gas of rubidium Rydberg atoms. Molecular potentials in Hund's case (c) are calculated by diagonalization of an interaction matrix. We show how the strong ℓ-mixing due to long-range Rydberg-Rydberg interactions can lead to resonances in excitation spectra. Such resonances were first reported in [S.M. Farooqi et al., Phys. Rev. Lett. 91, 183002 (2003)], where single UV photon excitations from the 5s ground state occurred at energies corresponding to normally forbidden transitions or very far detuned from the atomic energies. Here, we focus our attention on resonances at energies corresponding to excited atom pairs (n - 1)p_3/2+(n + 1)p_3/2. Very good agreement between the theoretical and experimental lineshapes is found.