Absolute rate calculations: atom and proton transfers in hydrogen-bonded systems.

We calculate energy barriers of atom- and proton-transfer reactions in hydrogen-bonded complexes in the gas phase. Our calculations do not involve adjustable parameters and are based on bond-dissociation energies, ionization potentials, electron affinities, bond lengths, and vibration frequencies of the reactive bonds. The calculated barriers are in agreement with experimental data and high-level ab initio calculations. We relate the height of the barrier with the molecular properties of the reactants and complexes. The structure of complexes with strong hydrogen bonds approaches that of the transition state, and substantially reduces the barrier height. We calculate the hydrogen-abstraction rates in H-bonded systems using the transition-state theory with the semiclassical correction for tunneling, and show that they are in excellent agreement with the experimental data. H-bonding leads to an increase in tunneling corrections at room temperature.     

Metal-organic frameworks: structural, energetic, electronic, and mechanical properties

The structural, energetic, electronic, and mechanical properties of a series of metal-organic framework (MOF) materials have been systematically studied with the density functional based tight-binding method. The cubic array of Zn(4)O(CO2)6 units (connectors) connected by different types of organic secondary building blocks (linkers) was considered. The results show that these materials are stable with bulk moduli ranging from 0.5 to 24 GPa with decreasing size of the linker. All MOFs are semiconductors or insulators with band gaps between 1.0 and 5.5 eV, mainly determined by highest occupied molecular orbital-lowest unoccupied molecular orbital gaps of the linker molecules. The atomic charges are nearly the same for free building blocks and the solid MOFs.     

Absolute rate constants for reactions of tributylstannyl radicals with bromoalkanes, episulfides, and alpha-halomethyl-episulfides, -cyclopropanes, and -oxiranes: new rate expressions for sulfur and bromine atom abstraction

Arrhenius rate expressions were determined for the abstraction of bromine atom from 2-phenethyl bromide by tri-n-butylstannyl radical (Bu(3)Sn(*)) in benzene using transient absorption spectroscopy, (log(k(abs,Br)/M(-1) s(-1)) = (9.21 +/- 0.20) - (2.23 +/- 0.28)/theta, theta = 2.3RT kcal/mol, errors are 2sigma) and for the abstraction of sulfur atom from propylene sulfide to form propylene, (log(k(s)/M(-1) s(-1)) = (8.75 +/- 0.91) - (2.35 +/-1.33)/theta). Rate constants for reactions of organic bromides, RBr, with Bu(3)Sn(*) were found to vary as R = benzyl (15.6) > thiiranylmethyl (6.2) > oxiranylmethyl (3.1) > cyclopropylmethyl (1.3) > 2-phenethyl (1.0), with k(abs,Br) = 6.8 x 10(7) M(-1) s(-1) at 353 K for 2-phenethyl bromide. Bromine abstraction from alpha-bromomethylthiirane is about 7-fold faster than sulfur atom abstraction and is comparable to the reactivity of a secondary alkyl bromide. The potential surface for the vinylthiomethyl --> allylthiyl radical rearrangement at UB3LYP/6-31G(d) and UB3LYP/6-311+G(2d,2p) levels of theory suggests that the thiiranylmethyl radical is produced about 9 kcal/mol above the allylthiyl radical on the rearrangement surface, consistent with the observed enhancement of the Br atom abstraction from the thiirane and with synchronous C-S bond scission of the thiirane ring. The selectivities reported in this work for S vs Cl and Br abstraction provide applications for radical-based synthesis and new competition basis rate expressions for trialkylstannyl radicals.     

Ab initio molecular orbital calculations of the energetic,structural, vibrational and electronic properties of some hydrogen bonded complexes of water,ammonia and hydroxylamine

Recently published results of some ab initio molecular orbital calculations on 10 hydrogen bonded homodimers and heterodimers of water, ammonia and hydroxylamine have been analysed. The properties discussed include the interaction energies, the structural parameters of the hydrogen bonded fragments, RAH⋯B, the vibrational properties (wavenumbers of the bonded AH-stretching and RAH-bending vibrational modes, and their shifts, and the wavenumbers of the highest frequency intermolecular modes of the complexes), and the atomic polar tensors, their invariants, and the Mulliken charges of the bonded hydrogen atoms. It is concluded that such complexes are stabilized by hydrogen bonds of the OH⋯N, OH⋯O and NH⋯N type, listed in decreasing order of strength. The complexes tend to form preferentially open (more or less linear) structures, followed by large cyclic structures, in which ring strain is minimized, and finally small cyclic structures, in which ring strain is more important.     

Absolute rate constants for some hydrogen atom abstraction reactions by a primary fluoroalkyl radical in water

A combination of laser flash photolysis and competitive kinetic methods have been used to measure the absolute bimolecular rate constants for hydrogen atom abstraction in water from a variety of organic substrates including alcohols, ethers, and carboxylic acids by the perfluoroalkyl radical, *CF(2)CF(2)OCF(2)CF(2)SO(3)(-) Na(+). Comparison, where possible, of these rate constants with those previously measured for analogous reactions in the non-polar organic solvent, 1,3-bis(trifluoromethyl)benzene (J. Am. Chem. Soc, 1999, 121, 7335) show that the alcohols react 2-5 times more rapidly in the water solvent and that the ethers react at the same rate in both solvents. A transition state for hydrogen abstraction that is more reminiscent of an "intimate ion pair" than a "solvent separated ion pair" is invoked to explain these modest solvent effects.     

Theoretical analysis of structural, energetic, electronic, and defect properties of Li2O

The structural, energetic, and electronic properties of stoichiometric and defective Li(2)O were studied theoretically. The reliability of the Perdew-Wang method in the framework of density functional theory (DFT), and of two DFT/Hartree-Fock hybrid methods (PW1PW and B3LYP), was examined by comparison of calculated and available experimental data. Atom-centered orbitals and plane waves were used as basis functions for the crystalline orbitals. For both cases, the basis set dependence of calculated properties was investigated. With most of the methods, good agreement with the experimental Li(2)O lattice parameter and cohesive energy was obtained. In accordance with experiment, the analysis of electronic properties shows that Li(2)O is a wide gap insulator. Among the considered methods, the hybrid methods PW1PW and B3LYP give the best agreement with experiment for the band gap. The formation of an isolated cation vacancy defect and an F center in Li(2)O were studied. The effect of local relaxation on the calculated defect formation energies and the defect-induced changes of electronic properties were investigated and compared to available experimental results. The migration of a Li(+) ion in Li(2)O bulk was investigated. The activation energy for the migration of a Li(+) ion from its regular tetrahedral site to an adjacent cation vacancy was calculated, including the effect of local relaxation. The calculated activation barriers, 0.27-0.33 eV, are in excellent agreement with experiment.     

Absolute rate constants for the reactions between amino and alkyl radicals at 298 K

The absolute rate constants for the reactions of NH₂ radicals with ethyl, isopropyl, and t-butyl radicals have been measured at 298 K, using a flash photolysis–laser resonance absorption method. Radicals were generated by flashing ammonia in the presence of an olefin. A new measurement of the NH₂ extinction coefficient and oscillator strength at 597.73 nm was performed. The decay curves were simulated by adjusting the rate constants of both the reaction of NH₂ with the alkyl radical and the mutual interactions of alkyl radicals. The results are k(NH₂ + alkyl) = 2.5 (±0.5), 2.0 (±0.4), and 2.5 (±0.5) × 10¹⁰ M^?1·s^?1 for ethyl, isopropyl, and t-butyl radicals, respectively. The best simulations were obtained when taking k(alkyl + alkyl) = 1.2, 0.6, and 0.65 × 10¹⁰M^?1·s^?1 for ethyl, isopropyl, and t-butyl radicals, respectively, in good agreement with literature values.     

Aromaticity and stability going in opposite directions: An energetic,structural, magnetic and electronic study of aminopyrimidines

The relation between molecular energetics and aromaticity was investigated for the interaction between the amino functional group and the nitrogen atoms of the pyridine and pyrimidine rings, using experimental thermodynamic techniques and computational geometries, enthalpies, chemical shifts, atomic charges and the Quantum Theory of Atoms in Molecules. 2,4-diaminopyrimidine and 2,4,6-triaminopyrimidine were studied by static bomb combustion calorimetry and Knudsen effusion technique. The derived gaseous-phase enthalpies of formation together with the enthalpies of formation of the three isomers of aminopyridine reported in the literature, were compared with the calculated computationally ones and extended to other diamino- and triaminopyrimidine isomers using the MP2/6-311++G(d,p) level of theory.The results were analyzed in terms of enthalpy of interaction between substituents and, due to the absence of meaningful stereochemical hindrance, strong inductive effects, or intramolecular hydrogen bonds according to QTAIM results, the resonance electron delocalization plays an almost exclusive role in the very exothermic enthalpies obtained. Therefore, this enthalpy of interaction was used as an experimental energetic measure of resonance effects and analyzed in terms of aromaticity. It was found that more conjugation between substituents means less aromaticity according to the magnetic (NICS) and electronic (Shannon) criteria, but more aromaticity according to the geometric (HOMA) criterion.     

ESR and calculations on electronic structure of phenalenyl and phenalenyl derivative radicals

Calculations on electronic structure of the perinaphthenyl radical and phenalenyl derivative radicals responsible for the composition of the ESR spectrum of marine diesel under heating were performed to obtain support for the experimental ESR results. The parameters calculated were the hyperfine coupling constants (A), which were then used for comparison with the experimental data. The energy‐minimized structures were obtained using the density functional theory method. In all cases, the symmetry system was taken into account in theoretical calculations. The differences between experimental and theoretical values were below 7% for nearest hydrogens in molecules, named hyperfine coupling constant A (first neighbors) and 18% for farthest hydrogens atoms named hyperfine coupling constants A′ (second neighbors), for all structures analyzed. Copyright © 2014 John Wiley & Sons, Ltd.     

Interaction between LiH molecule and Li atom from state-of-the-art electronic structure calculations

State-of-the-art ab initio techniques have been applied to compute the potential energy surface for the lithium atom interacting with the lithium hydride molecule in the Born-Oppenheimer approximation. The interaction potential was obtained using a combination of the explicitly correlated unrestricted coupled-cluster method with single, double, and noniterative triple excitations [UCCSD(T)-F12] for the core-core and core-valence correlation and full configuration interaction for the valence-valence correlation. The potential energy surface has a global minimum 8743 cm(-1) deep if the Li-H bond length is held fixed at the monomer equilibrium distance or 8825 cm(-1) deep if it is allowed to vary. In order to evaluate the performance of the conventional CCSD(T) approach, calculations were carried out using correlation-consistent polarized valence X-tuple-zeta basis sets, with X ranging from 2 to 5, and a very large set of bond functions. Using simple two-point extrapolations based on the single-power laws X(-2) and X(-3) for the orbital basis sets, we were able to reproduce the CCSD(T)-F12 results for the characteristic points of the potential with an error of 0.49% at worst. The contribution beyond the CCSD(T)-F12 model, obtained from full configuration interaction calculations for the valence-valence correlation, was shown to be very small, and the error bars on the potential were estimated. At linear LiH-Li geometries, the ground-state potential shows an avoided crossing with an ion-pair potential. The energy difference between the ground-state and excited-state potentials at the avoided crossing is only 94 cm(-1). Using both adiabatic and diabatic pictures, we analyze the interaction between the two potential energy surfaces and its possible impact on the collisional dynamics. When the Li-H bond is allowed to vary, a seam of conical intersections appears at C(2v) geometries. At the linear LiH-Li geometry, the conical intersection is at a Li-H distance which is only slightly larger than the monomer equilibrium distance, but for nonlinear geometries it quickly shifts to Li-H distances that are well outside the classical turning points of the ground-state potential of LiH. This suggests that the conical intersection will have little impact on the dynamics of Li-LiH collisions at ultralow temperatures. Finally, the reaction channels for the exchange and insertion reactions are also analyzed and found to be unimportant for the dynamics.     

Excited electronic state calculations by the transcorrelated variational Monte Carlo method: application to a helium atom

We have implemented the excited electronic state calculations for a helium atom by the transcorrelated variational Monte Carlo (TC-VMC) method. In this method, Jastrow-Slater-type wave function is efficiently optimized not only for the Jastrow factor but also for the Slater determinant. Since the formalism for the TC-VMC method is based on the variance minimization, excited states as well as the ground state calculations are feasible. It is found that both the first and the second excitation energies given by TC-VMC are much closer to the experimental data than those given by the variational Monte Carlo method with using the Hartree-Fock orbitals. The successful results in the TC-VMC method are considered to be due to the nodal optimization of the wave functions.     

Nucleophilic character of alkyl radicals—XIII: Absolute rate constants for the addition of alkyl radicals to acrylonitrile and methyl acrylate

The absolute rate constants for the addition of alkyl radicals to acrylonitrile and methyl acrylate are determined by evaluating the ratio of ligand-transfer oxidation and addition to the double bond. Secondary alkyl radi$\text{c}\text{?}$als appear to be more reactive than primary alkyl radicals, despite the less favourable energetics. The classical selectivity : reactivity relationship is reversed owing to the nucleophilic character of the alkyl radicals.     

Ab initio calculations of structural, elastic, and electronic properties of silver nitrides

The all-electron approach implemented in the CRYSTAL06 program is used along with a pseudopotential method in the pseudo-atomic orbital basis set to study the crystal structure, elastic constants and bulk moduli, the band structure and density of states for the family of silver nitrides. Calculations are performed within density functional theory with the use of local and gradient functionals to describe exchange and correlation. For the general type of the cubic lattice, all considered compounds can be put in the following order of their relative stability: AgN (rock salt structure), AgN₂ (fluorite structure), Ag₂N (cuprite structure), and Ag₃N (anti-ReO₂). It is shown that AgN, AgN₂, and Ag₂N are metals, whereas Ag₃N is a semiconductor with a band gap of 0.25 eV. Chemical bonding in these compounds has ionic and covalent components, apart from the metal one.     

Absolute rate constants for some intermolecular reactions of alpha-aminoalkylperoxyl radicals. Comparison with alkylperoxyls

Seven alpha-aminoalkylperoxyl radicals have been generated by 355 nm laser flash photolysis (LFP) of oxygen-saturated di-tert-butyl peroxide containing mono-, di-, and trialkylamines and a dialkylarylamine. All these peroxyls possess absorptions in the near-UV (strongest for the trialkylamine-derived peroxyls) which permits direct monitoring of the kinetics of their reactions with many substrates. The measured rate constants for hydrogen atom abstraction from some phenols and oxygen atom transfer to triphenylphosphine demonstrated that all seven alpha-aminoalkylperoxyls have similar reactivities toward each specific substrate. More importantly, a comparison with literature data for alkylperoxyls shows that alpha-aminoalkylperoxyls and these alkylperoxyls have essentially the same reactivities. The combination of LFP and alkylamines provides a quick, reliable method for determining absolute rate constants for alkylperoxyl radical reactions, an otherwise laborious task.     

Absolute rate constants for the addition of hydroxymethyl radicals to alkenes in methanol solution

Absolute rate constants and their temperature dependencies were determined for the addition of hydroxymethyl radicals (CH₂OH) to 20 mono- or 1,1-disubstituted alkenes (CH₂ = CXY) in methanol by time-resolved electron spin resonance spectroscopy. With the alkene substituents the rate constants at 298 K (k₂₉₈) vary from 180 M^?1s^?1 (ethyl vinylether) to 2.1 middot; 10⁶ M^?1s^?1 (acrolein). The frequency factors obey log A/M^?1s^?1 = 8.1 ± 0.1, whereas the activation energies (E_a) range from 11.6 kJ/mol (methacrylonitrile) to 35.7 kJ/mol (ethyl vinylether). As shown by good correlations with the alkene electron affinities (EA), log k₂₉₈/M^?1s^?1 = 5.57 + 1.53 · EA/eV (R² = 0.820) and E_a = 15.86 ? 7.38 · EA/eV (R² = 0.773), hydroxymethyl is a nucleophilic radical, and its addition rates are strongly influenced by polar effects. No apparent correlation was found between E_a or log k₂₉₈ with the overall reaction enthalpy. © 1995 John Wiley & Sons, Inc.     

A critical analysis of electronic density functionals for structural,energetic, dynamic,and magnetic properties of hydrogen fluoride clusters

We present extensive computational results on density functional calculations for hydrogen fluoride species (HF)_n (with 1≤n≤6) and compare them to results from other approaches and experiments, where available. Among the calculated properties we discuss equilibrium structural parameters, vibrational frequencies, electric dipole moments, IR intensities, dissociation energies, barriers for rearrangement by proton tunneling, NMR chemical shifts and spin couplings for ¹H and ¹⁹F, and magnetic susceptibilities. It is found that density functional (particularly BLYP) and even more so hybrid approaches (particularly B3LYP) provide useful results. However, we show that due to some characteristic deficiencies, these are in general not competitive with more quantitative results from large basis set MP2 calculations. The calculated magnetic properties do not indicate any “aromaticity” connected to a hypothetical electronic ring current. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1695–1719, 1997     

Absolute rate constants for reactions of free radicals in the high-temperature photolysis of formamide vapor. II. Amino radicals

The rotating-sector method has been applied to the photoinitiated radical-chain decomposition of formamide at 300°C to measure the rate constant for the bimolecular disappearance of NH₂ radicals. The decomposition is propagated by the reactions (1) (2) Conditions were chosen so that reaction (1) was rate controlling and NH₂ the terminating radical. A flow system was employed with C₂F₆ as a carrier gas at a pressure of 300 Tort, and the chain reaction was initiated by the photolysis of either formamide or NH₃. A value of 4.7(±2.0) × 10¹⁰ (M ·sec)^?1 was estimated for the termination reaction (3) and a value of 8.4 × 10⁶ (M ·sec)^?1 for reaction (1) in the same system, both at 300°C.     

Absolute rate constant for the disproportionation reaction of formyl radicals from 295 to 475 K

The rate constant for the reaction HCO + HCO → CH₂O + CO was measured at temperatures between 298 and 475 K. The formyl radicals were produced by flash photolysis of formaldehyde and were detected by resonance absorption at 614.5 nm. At low pressure and room temperature, k₁ = (3.35 ± 0.85) × 10^?11 cm³ molecule^?1 s^?1. There is no discernable variation of k₁ with temperature up to 475 K.