An experimental, computational, and uncertainty analysis study of the rates of iodoalkane trapping by DABCO in solution phase organic media.

NMR spectroscopy was used to measure the rates of the first and second substitution reactions between iodoalkane (R = Me, 1-butyl) and DABCO in methanol, acetonitrile and DMSO. Most of the reactions were recorded at three different temperatures, which permitted calculation of the activation parameters from Eyring and Arrhenius plots. Additionally, the reaction rate and heat of reaction for 1-iodobutane + DABCO in acetonitrile and DMSO were also measured using calorimetry. To help interpret experimental results, ab initio calculations were performed on the reactant, product, and transition state entities to understand structures, reaction enthalpies and activation parameters. Markov chain Monte Carlo statistical sampling was used to determine a distribution of kinetic rates with respect to the uncertainties in measured concentrations and correlations between parameters imposed by a kinetics model. The reactions with 1-iodobutane are found to be slower in all cases compared to reactions under similar conditions for iodomethane. This is due to steric crowding around the reaction centre for the larger butyl group compared to methyl which results in a larger activation energy for the reaction.

Tracking the Chemical Evolution of Iodine Species Using Recurrent Neural Networks.

We apply recurrent neural networks (RNNs) to predict the time evolution of the concentration profile of multiple species resulting from a set of interconnected chemical reactions. As a proof of concept of our approach, RNNs were trained on a synthetic dataset generated by solving the kinetic equations of a system of aqueous inorganic iodine reactions that can follow after nuclear reactor accidents. We examine the minimum dataset necessary to obtain accurate predictions and explore the ability of RNNs to interpolate and extrapolate when exposed to previously unseen data. We also investigate the limits of our RNN by evaluating the robustness of the training initialization on our dataset.

Synthesis, Characterization, and Density Functional Theory Analysis of Uranium and Thorium Complexes Containing Nitrogen-Rich 5-Methyltetrazolate Ligands.

Two nitrogen-rich, isostructural complexes of uranium and thorium, (C5Me5)2U[η(2)-(N,N')-tetrazolate]2 (7) and (C5Me5)2Th[η(2)-(N,N')-tetrazolate]2 (8), containing 5-methyltetrazolate, have been synthesized and structurally characterized by single-crystal X-ray diffraction, electrochemical methods, UV-visible-near-IR spectroscopy, and variable-temperature (1)H NMR spectroscopy. Density functional theory (DFT) calculations yield favorable free energies of formation (approximately -375 kJ/mol) and optimized structures in good agreement with the experimental crystal structures. Additionally, calculated NMR chemical shifts of 7 and 8 are in good agreement with the variable-temperature (1)H NMR experiments. Time-dependent DFT calculations of both complexes yield UV-visible spectroscopic features that are consistent with experiment and provide assignments of the corresponding electronic transitions. The electronic transitions in the UV-visible spectroscopic region are attributed to C5Me5 ligand-to-metal charge transfer. The low-lying molecular orbitals of the tetrazolate ligands (∼2 eV below the HOMO) do not contribute appreciably to experimentally observed electronic transitions. The combined experimental and theoretical analysis of these new nitrogen-rich uranium and thorium complexes indicates the tetrazolate ligand behaves primarily as a σ-donor.

Applicability of density functional theory in reproducing accurate vibrational spectra of surface bound species.

The structural equilibrium parameters, the adsorption energies, and the vibrational frequencies of the nitrogen molecule and the hydrogen atom adsorbed on the (111) surface of rhodium have been investigated using different generalized-gradient approximation (GGA), nonlocal correlation, meta-GGA, and hybrid functionals, namely, Perdew, Burke, and Ernzerhof (PBE), Revised-RPBE, vdW-DF, Tao, Perdew, Staroverov, and Scuseria functional (TPSS), and Heyd, Scuseria, and Ernzerhof (HSE06) functional in the plane wave formalism. Among the five tested functionals, nonlocal vdW-DF and meta-GGA TPSS functionals are most successful in describing energetics of dinitrogen physisorption to the Rh(111) surface, while the PBE functional provides the correct chemisorption energy for the hydrogen atom. It was also found that TPSS functional produces the best vibrational spectra of the nitrogen molecule and the hydrogen atom on rhodium within the harmonic formalism with the error of -2.62 and -1.1% for the N-N stretching and Rh-H stretching frequency. Thus, TPSS functional was proposed as a method of choice for obtaining vibrational spectra of low weight adsorbates on metallic surfaces within the harmonic approximation. At the anharmonic level, by decoupling the Rh-H and N-N stretching modes from the bulk phonons and by solving one- and two-dimensional Schrödinger equation associated with the Rh-H, Rh-N, and N-N potential energy we calculated the anharmonic correction for N-N and Rh-H stretching modes as -31 cm(-1) and -77 cm(-1) at PBE level. Anharmonic vibrational frequencies calculated with the use of the hybrid HSE06 function are in best agreement with available experiments.

Unravelling the mechanism of the asymmetric hydrogenation of acetophenone by [RuX2(diphosphine)(1,2-diamine)] catalysts.

The mechanism of catalytic hydrogenation of acetophenone by the chiral complex trans-[RuCl2{(S)-binap}{(S,S)-dpen}] and KO-t-C4H9 in propan-2-ol is revised on the basis of DFT computations carried out in dielectric continuum and the most recent experimental observations. The results of these collective studies suggest that neither a six-membered pericyclic transition state nor any multibond concerted transition states are involved. Instead, a hydride moiety is transferred in an outer-sphere manner to afford an ion-pair, and the corresponding transition state is both enantio- and rate-determining. Heterolytic dihydrogen cleavage proceeds neither by a (two-bond) concerted, four-membered transition state, nor by a (three-bond) concerted, six-membered transition state mediated by a solvent molecule. Instead, cleavage of the H-H bond is achieved via deprotonation of the η(2)-H2 ligand within a cationic Ru complex by the chiral conjugate base of (R)-1-phenylethanol. Thus, protonation of the generated (R)-1-phenylethoxide anion originates from the η(2)-H2 ligand of the cationic Ru complex and not from NH protons of a neutral Ru trans-dihydride complex, as initially suggested within the framework of a metal-ligand bifunctional mechanism. Detailed computational analysis reveals that the 16e(-) Ru amido complex [RuH{(S)-binap}{(S,S)-HN(CHPh)2NH2}] and the 18e(-) Ru alkoxo complex trans-[RuH{OCH(CH3)(R)}{(S)-binap}{(S,S)-dpen}] (R = CH3 or C6H5) are not intermediates within the catalytic cycle, but rather are off-loop species. The accelerative effect of KO-t-C4H9 is explained by the reversible formation of the potassium amidato complexes trans-[RuH2{(S)-binap}{(S,S)-N(K)H(CHPh)2NH2}] or trans-[RuH2{(S)-binap}{(S,S)-N(K)H(CHPh)2NH(K)}]. The three-dimensional (3D) cavity observed within these molecules results in a chiral pocket stabilized via several different noncovalent interactions, including neutral and ionic hydrogen bonding, cation-π interactions, and π-π stacking interactions. Cooperatively, these interactions modify the catalyst structure, in turn lowering the relative activation barrier of hydride transfer by ~1-2 kcal mol(-1) and the following H-H bond cleavage by ~10 kcal mol(-1), respectively. A combined computational study and analysis of recent experimental data of the reaction pool results in new mechanistic insight into the catalytic cycle for hydrogenation of acetophenone by Noyori's catalyst, in the presence or absence of KO-t-C4H9.

Electro-reduction of nitrogen on molybdenum nitride: structure, energetics, and vibrational spectra from DFT.

We used density functional theory to study the electrochemical conversion of nitrogen to ammonia on the (001), (100/010), (101), and (111) surfaces of γ-Mo2N. Based on the calculated free energy profiles for the reduction of nitrogen by the associative and dissociative mechanisms, reactivity was found to decrease in the order (111) > (101) > (100/010) ≈ (001). Namely, the cell potentials needed to drive the reduction to ammonia increase in the following order: -0.7 V on (111), -1.2 V on (101), and -1.4 V on (100/010) and (001) surfaces. The (111) surface was found to be the most reactive for nitrogen due to (i) its ability to adsorb the N2 in the side-on position which activates N-N bonding and (ii) its high affinity for N-adatoms which also prevents accumulation of H-adatoms on the catalytic surface at low cell potentials. We have also calculated vibrational frequencies of different NxHy species adsorbed on various γ-Mo2N surfaces. The frequencies are found to depend strongly on the type of the binding sites available on the crystal facets. A comparison of the calculated frequencies with the frequencies of the corresponding species in transition metal complexes and other metal surfaces shows that the frequencies of several signature modes fall in a similar region and might be used to assign the spectra of hydrogen and nitrogen containing surface species on different metal surfaces.

In situ X-ray pair distribution function analysis of geopolymer gel nanostructure formation kinetics.

With the ever-increasing environmentally-driven demand for technologically advanced structural materials, geopolymer cement is fast becoming a viable alternative to traditional cements due to its proven engineering characteristics and the reduction in CO2 emitted during manufacturing (as much as 80% less CO2 emitted in manufacture, compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of reaction responsible for nanostructural evolution during the geopolymerisation process. Here, in situ X-ray total scattering measurements and pair distribution function (PDF) analysis are used to quantify the extent of reaction as a function of time for alkali-activated metakaolin/slag geopolymer binders, including the impact of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerisation reaction. Quantifying the reaction process in situ from X-ray PDF data collected during the initial ten hours can provide an estimate of the total reaction extent, but when combined with data obtained at longer times (128 days here) enables more accurate determination of the overall rate of reaction. To further assess the initial stages of the geopolymerisation reaction process, a pseudo-single step first order rate equation is fitted to the extent of reaction data, which reveals important mechanistic information regarding the role of free silica in the activators in the evolution of the binder systems. Hence, it is shown that in situ X-ray PDF analysis is an ideal experimental local structure tool to probe the reaction kinetics of complex reacting systems involving transitions between disordered/amorphous phases, of which geopolymerisation is an important example.

First-principles prediction of the effects of temperature and solvent selection on the dimerization of benzoic acid.

We introduce a procedure of quantum chemical calculations (B3P86/6-31G**) to study carboxylic acid dimerization and its correlation with temperature and properties of the solvent. Benzoic acid is chosen as a model system for studying dimerization via hydrogen bonding. Organic solvents are simulated using the self-consistent reaction field (SCRF) method with the polarized continuum model (PCM). The cyclic dimer is the most stable structure both in gas phase and solution. Dimer mono- and dihydrates could be found in the gas phase if acid molecules are in contact with water vapor. However, the formation of these hydrated conformers is very limited and cyclic dimer is the principal conformer to coexist with monomer acid in solution. Solvation of the cyclic dimer is more favorable compared to other complexes, partially due to the diminishing of hydrogen bonding capability and annihilation of dipole moments. Solvents have a strong effect on inducing dimer dissociation and this dependence is more pronounced at low dielectric constants. By accounting for selected terms in the total free energy of solvation, the solvation entropy could be incorporated to predict the dimer behavior at elevated temperatures. The temperature dependence of benzoic acid dimerization obtained by this technique is in good agreement with available experimental measurements, in which a tendency of dimer to dissociate is observed with increased temperatures. In addition, dimer breakup is more sensitive to temperature in low dielectric environments rather than in solvents with a higher dielectric constant.

Investigation of formally zerovalent Triphos iron complexes.

The reduction of Triphos [PhP(CH(2)CH(2)PPh(2))(2)] iron halide complexes has been explored, yielding formally zerovalent (κ(3)-Triphos)Fe(κ(2)-Triphos) and (κ(3)-Triphos)Fe(κ(2)-Bpy). Electrochemical analysis, coupled with the metrical parameters of (κ(3)-Triphos)Fe(κ(2)-Bpy), reveal an electronic structure consistent with a π-radical monoanion bipyridine chelate that is antiferromagnetically coupled to a low spin, Fe(I) metal center.

Iron complex-catalyzed ammonia-borane dehydrogenation. A potential route toward B-N-containing polymer motifs using earth-abundant metal catalysts.

Ammonia-borane (NH(3)BH(3), AB) has garnered interest as a hydrogen storage material due to its high weight percent hydrogen content and ease of H(2) release relative to metal hydrides. As a consequence of dehydrogenation, B-N-containing oligomeric/polymeric materials are formed. The ability to control this process and dictate the identity of the generated polymer opens up the possibility of the targeted synthesis of new materials. While precious metals have been used in this regard, the ability to construct such materials using earth-abundant metals such as Fe presents a more economical approach. Four Fe complexes containing amido and phosphine supporting ligands were synthesized, and their reactivity with AB was examined. Three-coordinate Fe(PCy(3))[N(SiMe(3))(2)](2) (1) and four-coordinate Fe(DEPE)[N(SiMe(3))(2)](2) (2) yield a mixture of (NH(2)BH(2))(n) and (NHBH)(n) products with up to 1.7 equiv of H(2) released per AB but cannot be recycled (DEPE = 1,2-bis(diethylphosphino)ethane). In contrast, Fe supported by a bidentate P-N ligand (4) can be used in a second cycle to afford a similar product mixture. Intriguingly, the symmetric analogue of 4 (Fe(N-N)(P-P), 3), only generates (NH(2)BH(2))(n) and does so in minutes at room temperature. This marked difference in reactivity may be the result of the chemistry of Fe(II) vs Fe(0).

Importance of out-of-state spin-orbit coupling for slow magnetic relaxation in mononuclear Fe(II) complexes.

Two mononuclear high-spin Fe(II) complexes with trigonal planar ([Fe(II)(N(TMS)(2))(2)(PCy(3))] (1) and distorted tetrahedral ([Fe(II)(N(TMS)(2))(2)(depe)] (2) geometries are reported (TMS = SiMe(3), Cy = cyclohexyl, depe = 1,2-bis(diethylphosphino)ethane). The magnetic properties of 1 and 2 reveal the profound effect of out-of-state spin-orbit coupling (SOC) on slow magnetic relaxation. Complex 1 exhibits slow relaxation of the magnetization under an applied optimal dc field of 600 Oe due to the presence of low-lying electronic excited states that mix with the ground electronic state. This mixing re-introduces orbital angular momentum into the electronic ground state via SOC, and 1 thus behaves as a field-induced single-molecule magnet. In complex 2, the lowest-energy excited states have higher energy due to the ligand field of the distorted tetrahedral geometry. This higher energy gap minimizes out-of-state SOC mixing and zero-field splitting, thus precluding slow relaxation of the magnetization for 2.

Mechanistic aspects of propene epoxidation by hydrogen peroxide. Catalytic role of water molecules, external electric field, and zeolite framework of TS-1.

We have assessed various aspects of the epoxidation of propene by hydrogen peroxide, a reaction of considerable industrial importance, and elucidated some of the important factors that govern its mechanism. Quantum chemical calculations on the reactants, products, and transition states were performed both in the gas phase and using models to represent the TS-1 (titanosilicalite-1) catalyst. The reaction energy for the uncatalyzed process is computed as -52.6 kcal/mol with a barrier of 35.2 kcal/mol in the gas phase using the B3LYP hybrid density functional and a 6-31+G(d,p) basis set. The reaction appears to occur via a concerted mechanism. The competing reaction of ionic addition of hydrogen peroxide to the double bond to form a hydroperoxopropane is computed to have a reaction energy of only -17.1 kcal/mol with a barrier of 34.8 kcal/mol and is therefore expected not to be thermodynamically preferable. Introduction of water molecules to the model is calculated to reduce the reaction barrier to 25.7 kcal/mol in the case of a single molecule but did not significantly affect the reaction energy. The competing addition reaction barrier appears to be significantly less sensitive to the presence of water molecules, suggesting that the concerted epoxidation reaction is also kinetically favored in the polar environment. Introduction of additional water molecules does not result in a noticeable enhancement. The water molecules appear to mediate proton transfer between the peroxide oxygens in the rate determining step of the concerted epoxidation reaction. The introduction of a background solvent field was also found to reduce the activation energy. For example, a model with a single explicit water molecule and the solvent field gives an activation barrier of 16.9 kcal/mol. A similar effect is observed if an external electric field is applied to the model with the dipole component directed along the O-O bond direction. Calculations were also performed on the same reaction occurring in the vicinity of a model for the active site of the TS-1 catalyst using a cluster model. The activation barrier for the cluster model is calculated to be 25.8 kcal/mol with a reaction energy of -55.5 kcal/mol, which is comparable to the gas phase model with a single water molecule added. No significant changes are observed with the addition of water molecules in this model.

A mechanism for the decomposition of dinitropropyl compounds.

A decomposition mechanism is proposed for 2,2-dinitro-1-methoxypropane, a compound whose structure resembles the nitroplasticizer (NP) component of plastic-bonded explosive PBX 9501. A library of key reactions is presented and is based on the results of NP aging studies and existing decomposition mechanisms for similar nitro compounds. Density functional electronic structure calculations on these reactions were used to develop a decomposition mechanism at lower temperatures, which begins with HONO elimination and leads to intermediates that can produce CO, CO(2), NO, and N(2)O gases. These gases were observed in low temperature (48 to 64 degrees C) aging studies of NP. A high temperature mechanism involving NO(2) scission is compared to a thermal decomposition mechanism determined by simultaneous thermogravimetric modulated beam mass spectrometry. The calculated energy barriers for HONO elimination and NO(2) scission in the gas phase are reported and compared to experimental results.